Organisationseinheit: Deutschland. Umweltbundesamt. Fachgebiet II.1.4 - Mikrobiologische Risiken
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Bridging disciplines towards wastewater-based surveillance of antimicrobial resistance: frequency, local dynamics, and genomic characteristics of carbapenemase-producing Klebsiella pneumoniae
(2026) Werner, Katharina; Bajic, Vladimir; Blumenscheit, Christian; Baum, David; Desirò, Daniel; Sedaghatjoo, Somayyeh; Barthelmes, Jeanette; Liebschner, Anne-Kathrin; Förster, Christina; Fuchs, Stephan; Bethe, Astrid; Walther, Birgit
The World Health Organization (WHO) has designated carbapenemase-producing Klebsiella pneumoniae (CP-KP) as a critical priority pathogen due to its increasing importance for human health. As wastewater-based surveillance (WBS) is discussed as a complementary tool for classical systems regarding hazard forecasting and early-warning, we designed a “wet-lab to genomics” workflow to target CP-KP in raw influent wastewater samples to support method development processes across different scientific disciplines.
The CP-KP screening workflow was set up based on membrane filtration, selective chromogenic media for selective cultivation and the modified carbapenem inactivation method (mCIM) for confirming carbapenemase-production using 33 samples from four different wastewater treatment plants in North-Eastern Germany. All samples tested positive for CP-KP, with concentrations ranging between 102 and 104 colony-forming units (cfu) per 100 ml across the sample set. As a result, 320 isolates belonged to the Klebsiella, Enterobacter, Citrobacter (KEC)- group, with the majority being identified as KP (n= 297; 93%), including n= 253 (79%) verified CP-KP. Genotypic characterization of CP-KP by PCR revealed the predominance of blaOXA-48-related genes (n= 83) among isolates from all WWTPs.
As quality parameters, colony counts for viable Escherichia coli (EC) were employed as a proxy for valid wastewater samples and extended-spectrum beta-lactamase-producing E. coli (ESBL-EC) as indicator for AMR, with cfu/100 ml ranges from 10⁶ to 10⁷ and 102 to 10⁴, respectively. To verify the screening outcome, a subset of 58 CP-KP from two WWTPs were subjected to whole genome sequencing (WGS). As a result, eight different sequence types (STs), i.e., ST147 and ST273 (both: clonal group 147), ST258, ST35, ST15, ST37, ST307, and ST485 were identified. These include clinically relevant STs clustering closest with fecal isolates from Germany when compared with Pathogenwatch-database entries. Moreover, WGS data enabled the identification of antibiotic resistance genes (ARGs), and the detection of closely related isolates within the WWTP dataset. © Authors
A metagenomic analysis of urban river samples reveals high numbers of sequences related to mycoviruses
(2026) Zell, Roland; Groth, Marco; Selinka, Lukas; Selinka, Hans-Christoph
Mycoviruses have been classified into 35 virus families so far. In addition to numerous mycoviruses with proven fungal or oomycetes hosts, many newly discovered viruses from environmental water and soil samples and various animal or plant specimens exhibit significant similarity to classified mycoviruses, thereby expanding the known sequence space of fungal and related viruses. In this study, we searched for mycoviruses in two environmental water samples that had been collected from the Teltow Canal and the Havel River in Berlin, Germany. Viral sequences with similarity to members of 16 virus families were identified. The most common viruses in our samples were botourmia-like viruses with moderate similarity to members of the genus Ourmiavirus. Notably, 58 of the ourmia-like sequences from the Teltow Canal and Havel River and 10 ourmia-like sequences from other sources exhibited a dicistronic genome layout. The second open reading frame (ORF) of these viruses encoded a putative capsid protein with an S domain that showed little similarity to the structural proteins of the classified ourmiaviruses. The second-largest virus group (59 sequences) was assigned to the order Ghabrivirales, and 13 of these sequences exhibited similarity to members of the suborder Alphatotivirineae (families Orthototiviridae, Pseudototiviridae, Botybirnaviridae, and Chrysoviridae). Thirty-three sequences clustered with members of the suborder Betatotivirineae – three of them with members of the family Artiviridae. Fifteen highly divergent toti-like sequences suggest the need to establish a new higher-order taxon within the order Ghabrivirales. Other virus sequences were assigned to the families Mitoviridae (three unuamitoviruses and 10 highly divergent mitovirus-like sequences), Narnaviridae (five "alphanarnavirus"-like sequences), Amalgaviridae (two zybavirus-like sequences), Hypoviridae (one partial RdRP sequence), and Mymonaviridae (one partial RdRP sequence), and one was not classified (Sclerophthora macrospora B-like virus). Notable results include a clade of highly divergent mitovirus-like sequences with a standard translation code, three narnavirus-like sequences with a reverse-frame ORF, and a clade of four Ghabrivirales-like replicase sequences that were found to have numerous termination codons regardless of which translation table was used. © The Author(s) 2026
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