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
Abwassersurveillance: der methodische Weg zur Vergleichbarkeit von Messergebnissen am Beispiel Influenzaviren
(2026) Kallies, René; Fretschner, Till; Zeisler, Edgar Elon; Scheller, Steffi; Aurenz, Andreas; Schneider, Beate; Lukas, Marcus; Braun, Ulrike; Greiner, Timo; Schumacher, Jakob; Selinka, Hans-Christoph; Walther, Birgit
Influenzaviren stellen durch saisonal wiederkehrende Infektionen verbunden mit ihrem Pandemiepotenzial eine Belastung für die öffentliche Gesundheit dar. Bestehende Überwachungssysteme können durch abwasserbasierte Epidemiologie (ABE) sinnvoll ergänzt werden. ABE hat sich als wertvolles Instrument etabliert, um das Vorkommen von Viren auf Bevölkerungsebene zu erfassen und zu bewerten. Die Detektion viralen Erbmaterials als Indikator für Viren im Abwasser ist herausfordernd, da verschiedene Parameter den jeweiligen Nachweis begrenzen können. Dieser Artikel diskutiert die Auswirkungen unterschiedlicher Methodenkombinationen auf die Analyseergebnisse zum Nachweis von Viren in Abwasser und zeigt, dass methodenabhängige Unterschiede die Nachweis und Quantifizierungsergebnisse erheblich beeinflussen. Die Arbeit unterstreicht die Notwendigkeit einer kontextbezogenen Interpretation sowie systematischer Methodenvergleiche für eine verlässliche Implementierung der ABE von Influenzaviren. Quelle: UMID : Umwelt und Mensch - Informationsdienst ; Umwelt & Gesundheit, Umweltmedizin, Verbraucherschutz / Boden- und Lufthygiene (Berlin) Institut für Wasser-. - Berlin. - (2026), Heft 1, Seite 2
Antibiotic prophylaxis and hospitalization of horses subjected to median laparotomy: gut microbiota trajectories and abundance increase of Escherichia
(2023) Kauter, Anne Maria Luise; Brombach, Julian; Lübke-Becker, Antina; Walther, Birgit
Introduction: Horse clinics are hotspots for the accumulation and spread of clinically relevant and zoonotic multidrug-resistant bacteria, including extended-spectrum (Beta)-lactamase producing (ESBL) Enterobacterales. Although median laparotomy in cases of acute equine colic is a frequently performed surgical intervention, knowledge about the effects of peri-operative antibiotic prophylaxis (PAP) based on a combination of penicillin and gentamicin on the gut microbiota is limited. Methods: We collected fecal samples of horses from a non-hospitalized control group (CG) and from horses receiving either a pre-surgical single-shot (SSG) or a peri-operative 5-day (5DG) course of PAP. To assess differences between the two PAP regimens and the CG, all samples obtained at hospital admission (t0), on days three (t1) and 10 (t2) after surgery, were screened for ESBL-producing Enterobacterales and subjected to 16S rRNA V1-V2 gene sequencing. Results: We included 48 samples in the SSG (n = 16 horses), 45 in the 5DG (n = 15), and 20 in the CG (for t0 and t1, n = 10). Two samples of equine patients receiving antibiotic prophylaxis (6.5%) were positive for ESBL-producing Enterobacterales at t0, while this rate increased to 67% at t1 and decreased only slightly at t2 (61%). Shannon diversity index (SDI) was used to evaluate alpha-diversity changes, revealing there was no significant difference between horses suffering from acute colic (5DG, SDImean of 5.90, SSG, SDImean of 6.17) when compared to the CG (SDImean of 6.53) at t0. Alpha-diversity decreased significantly in both PAP groups at t1, while at t2 the onset of microbiome recovery was noticed. Although we did not identify a significant SDImean difference with respect to PAP duration, the community structure (beta-diversity) was considerably restricted in samples of the 5DG at t1, most likely due to the ongoing administration of antibiotics. An increased abundance of Enterobacteriaceae, especially Escherichia, was noted for both study groups at t1. Conclusion: Colic surgery and PAP drive the equine gut microbiome towards dysbiosis and reduced biodiversity that is accompanied by an increase of samples positive for ESBL-producing Enterobacterales. Further studies are needed to reveal important factors promoting the increase and residency of ESBL-producing Enterobacterales among hospitalized horses. © 2023 Kauter, Brombach, Lübke-Becker, Kannapin, Bang, Franzenburg, Stoeckle, Mellmann, Scherff, Köck, Guenther, Wieler, Gehlen, Semmler, Wolf and Walther
One Health: Gesundheit von Mensch, Tier und Umwelt
(2023) Fiack, Suzan; Straff, Wolfgang; Walther, Birgit
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