Annual Conference 2025 of the Association for General and Applied Microbiology - Jahrestagung 2025 der Vereinigung für Allgemeine und Angewandte Mikrobiologie

PD Dr.

Chair

Collateral damage of antibiotic eradication targeting nasal Staphylococcus aureus requires alternative decolonization strategies

Microbial communities

Question: Staphylococcus aureus is a major human pathogen which causes a wide variety of infections. S. aureus colonizes approximately the nares of 20% of the human population. Decolonization treatments prior to invasive medical inventions lead to a reduced risk in subsequent infections. The proven method for decolonization of S. aureus is a treatment with the antibiotic mupirocin, which leads to problems on the long run. Firstly S. aureus recolonizes usually after the treatment has stopped. Secondly antibiotic resistance to mupirocin in S. aureus is emerging. In addition, S. aureus is part of a complex microbiome in the human nares. Other bacterial species have promoting or suppressive effects on S. aureus nasal colonization. The effect of mupirocin treatment on the nasal microbiome is poorly understood on the species and strain level. In this study we determine the global effect of nasal decolonization strategies on the nasal microbiome. Furthermore, we propose potential alternative methods with increased precision and selectivity.Methods: We used a combination of in vitro techniques and in silico prediction to determine antibiotic susceptibility and colonization dynamics upon mupirocin treatment of a comprehensive collection of nasal commensals. Furthermore, we validated our results with in vivo colonization data.Results: We show that presence of certain alleles of the mupirocin target explains antibiotic resistance across a wide variety of nasal commensals from very diverse phylogenetic clades. Presence of identified resistance determinants governs growth in a competitive in vitro system. Observed microbiome disturbances caused by mupirocin treatment correlate well with in vivo colonization data.Conclusion: We show that mupirocin treatment has notable collateral side effects on nasal commensals perturbing the composition of nasal microbiomes. Side effects are especially pronounced on other- often harmless - commensal staphylococci, which are frequently antagonizing S. aureus colonization. Hence, we propose alternative antimicrobial approaches targeting molecular structures which are unique to pathogenic commensals. A promising alternative could be bacteriophages, microbial viruses. In contrast to frequently used antibiotics bacteriophages target distinct surface structures that are unique to S. aureus allowing potentially selective and controlled eradication of this pathogens from the human nose.

Short lecture

Prof.

Towards informed antimicrobial use in aquaculture: How fish age, species and climate shape gut microbiome responses to florfenicol and peracetic acid

Environmental microbiology & ecology

IntroductionAntibiotics and antiparasitics are essential for managing infectious diseases in commercial aquaculture, particularly in high-density rearing systems like hatcheries. While antibiotics have been linked to increased abundance of antibiotic resistance genes and persistent shifts in the intestinal microbiome of farmed fish, the influence of underlying host factors (age, species), environmental determinants (climate) and co-application with antiparasitics on microbiome dynamics remains unclear.GoalsThis study focused on the effects of antimicrobial treatment on the gut microbiome of brown trout (Salmo trutta) and nile tilapia (Oreochromis niloticus), exploring the co-selective pressure of combined florfenicol (FF) and peracetic acid (PAA) on microbial composition and how host age, climate, and species shape the microbiome"s response to antimicrobial exposure.MethodsIn a freshwater recirculating system (9 – 11 °C), adult and juvenile brown trout were subjected to three treatments (10 mg/kg bw FF, FF+PAA, 0.005% PAA) compared to an untreated control group. Adult nile tilapia in a pond system (24 – 28 °C) received 10 mg/kg bw FF. Fecal samples were collected before treatment, on the last day of treatment (day 10) and four times during the post-treatment phase, followed by 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform.Results Fish age and species significantly shaped the gut microbiome response to FF and PAA treatment, with juvenile trout showing greater microbiome volatility than adults. Changes included declines in beneficial commensals (Cetobacterium, Lactococcus), whose network positions remained altered despite recovered abundance by day 28. FF impacts were enhanced in warmer climates, with shifts persisting up to day 30 and reduced bacterial diversity in tilapia. Aeromonas, Streptococcus and Cetobacterium were identified as common responders following FF treatment.SummaryAddressing a critical knowledge gap regarding the extent to which the response to antimicrobials is dependent on the developmental stage of the fish and rearing climate, our study emphasizes the importance of integrating gut microbiome characteristics related to fish age and species in aquaculture management practices. This study also provides the first evidence that external PAA application disrupts gut microbial communities, highlighting potential long-term consequences of combined use of antibiotics and antiparasitics.

Prof

Management of Lasiodiplodia theobromae, a mango dieback disease, in the UAE with the application of endophytic actinobacteria

Dieback induced by the fungus Lasiodiplodia theobromae is a significant affliction in mango farms inside the United Arab Emirates (UAE). This study identified 36 actinobacterial isolates from mango roots in the UAE, with 24 categorized as streptomycetes (SA) and 12 as non-streptomycetes (NSA). Eleven isolates (8 SA and 4 NSA) exhibited antagonistic activity against L. theobromae, attributed to the formation of diffusible antifungal metabolites, extracellular cell-wall-degrading enzymes (CWDEs), or both. Employing a "novel" mango fruit bioassay, all isolates were evaluated in vivo for their capacity to diminish lesion severity on fruits infected with L. theobromae. Three isolates, two from Streptomyces and one from Actinoplanes spp., had the most potent inhibitory action against this pathogen in vitro and were consequently chosen for testing on mango seedlings. Our findings indicated that the antifungal efficacy of Streptomyces UAE1 was linked to antibiosis, as well as the synthesis of CWDEs (namely, chitinase) and siderophores; conversely, Streptomyces UAE2 and Actinoplanes UAE1 were identified as being connected to antibiotic- and CWDE-production, respectively. Pre-inoculation in greenhouse studies with the most promising actinobacterial isolates yielded significant disease protection in mango seedlings later inoculated with the pathogen. The significant decrease in the estimated disease severity indices of mango dieback following individual biocontrol agent (BCA) treatments, in contrast to the pathogen alone, substantiates their efficacy in managing mango dieback disease. Mango seedlings infected with L. theobromae and treated with Streptomyces UAE1 exhibited a considerable reduction in both the number of defoliated leaves and the conidia counts of L. theobromae, decreasing by 3- and 6-fold, respectively, compared to the other two biocontrol agent treatments. This suggests that the synergistic antifungal properties of Streptomyces UAE1, employing several mechanisms, impeded the in planta invasion of L. theobromae. This is the first study on the effects of endophytic BCA against L. theobromae in mango seedlings utilizing endophytic microbial antagonists. This is the inaugural report of endophytic actinobacteria naturally present in UAE or elsewhere, demonstrating the capacity to inhibit mango dieback disease.

Prof. Dr.

Cross-kingdom interactions of Ustilago and Pseudomonas via secondary metabolites

Many fungal strains in the family Ustilaginaceae secrete itaconic acid (ITA) along with its derivatives, 2-hydroxyparaconate (2-HP) and itatartarate (ITT) under nitrogen limitation. While the antimicrobial properties of ITA are well documented, the ecological role of its derivatives remains largely unexplored. Notably, the bacterium Pseudomonas aeruginosa possesses a specialized ITA metabolic operon with genes not directly related to ITA degradation (PA0879-PA0881), but essential for tolerance to the ITA derivatives, suggesting a molecular arms race within their shared habitat (de Witt et al., 2023). This study aims to investigate how fungal secondary metabolites shape cross-kingdom communities and elucidate their effects on bacterial metabolism and tolerance, using the non-pathogenic strain P. putida KT2440, engineered to heterologously express the ITA metabolic operon from P. aeruginosa PAO1. Inhibition studies using Ustilago supernatants and purified 2-HP and ITT on different engineered Pseudomonas strains identified the uncharacterized ring-cleaving dioxygenase RdoPA (PA0880) as a key mediator of tolerance to ITA derivatives. Interestingly, the ITA synthesis clusters of several fungal strains, such as Ustilago maydis and Aspergillus terreus, contain genes with high sequence similarity to rdoPA (UMAG_12299, rdo1; ATEG_10557, rdoA). Complementation studies and biochemical characterization confirm that these evolutionarily distant enzymes share lactonase activity for the enantioselective conversion of (S)-2-HP to (S)-ITT. Combined with the finding that (S)-2-HP inhibits ITA degradation, this conversion clarifies RdoPA's physiological role in Pseudomonas, while its role in fungi, remains unclear. Preliminary results with eGfp-tagged Rdo variants in U. maydis revealed its localization to the mitochondria, and we currently hypothesize a self-protection mechanism against the ITA derivatives, potentially due to toxic side activities of mitochondrial enzymes. With a clearer understanding of the mode of action and tolerance mechanisms, future studies will employ rational genetic modifications to fine-tune fungal production and bacterial degradation of ITA and its derivatives, incorporating transporters to regulate metabolic flux (battle of rates). These targeted modifications aim to mimic the dynamic evolutionary interplay within the ecological niche in a synthetic co-culture, advancing our understanding about the rules of interaction.

Antimicrobial peptide import in E. coli as a defense mechanism

Membranes and transport

Part of the innate immune system, antimicrobial peptides (AMPs) are produced by virtually all types of cells in a bid to kill or control microbial adversaries. AMPs are being discussed as a new treatment option that promises to engender less development of resistance than existing antibiotics. Yet a variety of prokaryotic mechanisms for resistance against AMPs exist. We followed up on the idea that AMP import into the bacterial cytoplasm could operate as a defense mechanism. Using E. coli, we studied existing mechanisms for AMP import, focusing on a well-characterized transporter called sbmA. SbmA was known to render bacteria susceptible to proline-rich AMPs that act on internal targets, which we confirm using Apidaecin 1B as a model. Using Magainin 2, we show that sbmA simultaneously provides resistance to helical-amphipathic, ribosomally-produced AMPs that target bacterial membranes. Whether the presence of sbmA helps or hurts is thus contingent on the nature of the attacking peptide, hinting at an evolutionary arms race between attack and defence.

Prof.  Dr.

Antimicrobial-resistant Escherichia coli in irrigation water of different quality, and leaves of irrigated cilantro and alfalfa plants from the Mezquital Valley, Mexico

Background:Water scarcity has increased the use of wastewater (WW) for irrigation, especially in low/middle-income countries. However, WW irrigation poses risks, such as the spread of antimicrobial-resistant bacteria (ARBs) and pathogens like coliforms into the food chain. Humans are exposed to ARBs through cilantro consumption or indirectly via contact with alfalfa-fed livestock.Hypothesis and Material/Method:This study examined the presence of coliform ARBs in irrigation waters, including untreated WW (UWW), treated WW (TWW), groundwater (GW), spring water (SW), and irrigated crops (cilantro, alfalfa) collected in the Mezquital Valley, Mexico. We focused on the cultivation of bacteria colonizing the endosphere or strongly attached to the surface of leaves. We hypothesized that, (I) irrigation water quality influences the spread of coliform ARBs to plants, and (II) plants irrigated with TWW may harbour ARBs with a higher degree of multi-resistance due to potential horizontal gene transfer during WW treatment, compared to those irrigated with UWW, GW and SW.Result and Conclusion:Extended spectrum β-lactamase producing (ESBL) and carbapenem-resistant (CR) E. coli were cultivated by selective pre-enrichment and subsequent isolation on selective E. coli media. E. coli were identified by uidA PCR and MALDI-TOF MS. A total of 210 ESBL (130 alfalfa, 24 cilantro, 20 UWW, 18 per TWWs) and 40 CR E. coli (22 alfalfa, 14 UWW, 4 TWW) were isolated. ESBL/CR E. coli were not cultured from GW and SW. So far, WW treatment showed no significant effect on the multi-resistance of E. coli. Multi-resistance of E. coli isolated from alfalfa and cilantro was slightly lower compared to WW E. coli (without significant differences), depending on irrigation water quality or manure application[Office1] . Both, WW derived irrigation water and manure were determined as sources of multi-resistant E. coli in the studied crops. The E. coli strains will be characterized in more detail by genome sequencing.

Environmental microbiology & ecology II
Antimicrobial strategies and resistance

Appointment

Chair

Topic

Programme

Environmental microbiology & ecology IIAntimicrobial strategies and resistance

Appointment

Chair

Topic

Programme

Environmental microbiology & ecology II
Antimicrobial strategies and resistance