HUN-REN Biological Research Centre, Szeged 
Oct 2, 2025 | News
Roland Wirth and colleagues at the HUN-REN Biological Research Centre, Szeged, Institute of Plant Biology, Microbial and Plant Genomics Research Group, led by Gergely Maróti, investigated the prevalence and the potential human health effects of antibiotic resistance in the microbiome of the municipal wastewater treatment plant in Szeged. The study aimed the detailed mapping and characterization of the microbial communities present at various stages of wastewater treatment. The research revealed that the abundance of antibiotic resistance genes (ARGs) and their expression only partially correlated during the treatment process. The authors highlighted that human-associated pathogenic microbes – which carry the majority of clinically relevant ARGs – significantly decrease during wastewater treatment, particularly during anaerobic digestion, which effectively reduces both the relative abundance and activity of ARGs in multiple bacteria. At the same time, other microbial populations of non-human origin play an important role in maintaining and potentially spreading ARGs during the treatment process. The study was published in Water Research.
The genes conferring antibiotic resistance in microbes are fundamentally of ancient origin; however, human activities, such as the widespread use of antibiotics, impose selective pressure on resistant microbes. Consequently, the risk posed by clinically relevant, antibiotic-resistant pathogens continues to rise. Urban wastewater treatment plants, which employ a combination of activated sludge and anaerobic digestion, not only purify wastewater but also provide a bioremediation process that reduces pathogenic bacteria while producing sustainable energy in the form of biomethane. The decomposition of organic matter is time-consuming, and during this process, ARGs can be transferred between pathogenic and non-pathogenic microbial populations. Studying specific microbes in complex microbiomes is challenging since most microorganisms cannot survive when isolated and rely on intricate community interactions. This necessitates specialized approaches to identify ARG carrying microbes. Advances in metagenomic, metatranscriptomic, and bioinformatic methods now make it possible to overcome these challenges.
In this study, the authors reconstructed microbial genomes from samples of the Szeged wastewater treatment plant, identified the ARGs they carry, and assessed their expression at different treatment stages. This approach enabled not only the detection of ARGs but also the evaluation of their actual activity and potential clinical risk. The results showed that the wastewater microbiome is composed of complex microbial communities from multiple sources, including human and environmental populations. ARG-carrying microbes were classified as human-associated, environmental, or of unknown origin. During treatment, the relative abundance of pathogenic human-associated microbes decreased significantly, whereas environmental populations increased, indicating the formation of a distinct microbiome within the treatment system that may function as a gene reservoir.
Figure 1: Changes in the relative abundance of the most prevalent bacteria in the wastewater treatment microbiome and the antibiotic resistance genes (ARGs) they carry.
Among microbes adapted to the treatment environment, glycopeptide resistance was particularly prevalent. Most pathogenic and ARG-carrying microbes belonged to the Pseudomonadota phylum, with human-associated Enterobacteriaceae members being prominent, carrying ARGs of highest clinical concern (Figure 1). Importantly, genes conferring fluoroquinolone resistance remained active after treatment, representing a potential public health risk. Overall, the study demonstrates that wastewater treatment and anaerobic digestion effectively reduce human-associated, potentially pathogenic microbial populations and the most critical ARGs, while some key resistance genes, including fluoroquinolone resistance determinants, can remain active. This underscores that assessing public health risks requires not only the presence of ARGs but also their expression, the role of mobile genetic elements, and the presence and origin of pathogenic microbes within the wastewater system.