Artificial Intelligence-Driven Analysis of Antimicrobial-Resistant and Biofilm-Forming Pathogens on Biotic and Abiotic Surfaces.

The growing threat of antimicrobial-resistant (AMR) pathogens to human health worldwide emphasizes the need for more effective infection control strategies. Bacterial and fungal biofilms pose a major challenge in treating AMR pathogen infections. Biofilms are formed by pathogenic microbes encased in extracellular polymeric substances to confer protection from antimicrobials and the host immune system. Biofilms also promote the growth of antibiotic-resistant mutants and latent persister cells and thus complicate therapeutic approaches. Biofilms are ubiquitous and cause serious health risks due to their ability to colonize various surfaces, including human tissues, medical devices, and food-processing equipment. Detection and characterization of biofilms are crucial for prompt intervention and infection control. To this end, traditional approaches are often effective, yet they fail to identify the microbial species inside biofilms. Recent advances in artificial intelligence (AI) have provided new avenues to improve biofilm identification. Machine-learning algorithms and image-processing techniques have shown promise for the accurate and efficient detection of biofilm-forming microorganisms on biotic and abiotic surfaces. These advancements have the potential to transform biofilm research and clinical practice by allowing faster diagnosis and more tailored therapy. This comprehensive review focuses on the application of AI techniques for the identification of biofilm-forming pathogens in various industries, including healthcare, food safety, and agriculture. The review discusses the existing approaches, challenges, and potential applications of AI in biofilm research, with a particular focus on the role of AI in improving diagnostic capacities and guiding preventative actions. The synthesis of the current knowledge and future directions, as described in this review, will guide future research and development efforts in combating biofilm-associated infections.

In the footsteps of Heinz Schlesner and Peter Hirsch: Exploring the untapped diversity of the phylum Planctomycetota in isolates from the 1980s to the early 2000s.

Recent sampling and strain isolation campaigns have accelerated research on the bacterial phylum Planctomycetota. The contribution of more than 100 novel isolates to the open collection of currently 123 described planctomycetal species in the last decade benefited greatly from pioneering work conducted in the second half of the last century. One of those pioneers was Heinz Schlesner, who investigated budding and prosthecate bacteria from habitats world-wide during his time at Christian-Albrechts-University Kiel. An outcome of his research was a strain collection with more than 500 isolates belonging to different bacterial phyla, many of which are uncharacterised members of the phylum Planctomycetota. Due to the lack of affordable genome sequencing techniques at the time of their isolation, most of them were characterised based on phenotypic features and DNA-DNA hybridisation experiments. After the retirement of Heinz Schlesner in 2002, the collection was stored for several years and transferred to Jena in 2019. To get a glimpse on the diversity of members from the phylum Planctomycetota in Schlesner's collection, we here summarised from his records and publications all available information about the collection regarding sampling habitat and phylogeny. Furthermore, we conducted an updated phylogenetic analysis for a representative excerpt of the collection based on the 16S rRNA gene sequence of 59 strains Schlesner deposited in the NCBI database during strain characterisation studies published in the 1980s until the early 2000s. The results support that strains from his collection are still a valuable contribution to expand the cultivated diversity of the understudied phylum Planctomycetota.

Mixed Fungal Biofilms: From Mycobiota to Devices, a New Challenge on Clinical Practice.

Most current protocols for the diagnosis of fungal infections are based on culture-dependent methods that allow the evaluation of fungal morphology and the identification of the etiologic agent of mycosis. Most current protocols for the diagnosis of fungal infections are based on culture-dependent methods that enable the examination of the fungi for further identification of the etiological agent of the mycosis. The isolation of fungi from pure cultures is typically recommended, as when more than one species is identified, the second agent is considered a contaminant. Fungi mostly survive in highly organized communities that provoke changes in phenotypic profile, increase resistance to antifungals and environmental stresses, and facilitate evasion from the immune system. Mixed fungal biofilms (MFB) harbor more than one fungal species, wherein exchange can occur that potentialize the effects of these virulence factors. However, little is known about MFB and their role in infectious processes, particularly in terms of how each species may synergistically contribute to the pathogenesis. Here, we review fungi present in MFB that are commensals of the human body, forming the mycobiota, and how their participation in MFB affects the maintenance of homeostasis. In addition, we discuss how MFB are formed on both biotic and abiotic surfaces, thus being a significant reservoir of microorganisms that have already been associated in infectious processes of high morbidity and mortality.

Updates to the recently introduced family Lacipirellulaceae in the phylum Planctomycetes: isolation of strains belonging to the novel genera Aeoliella, Botrimarina, Pirellulimonas and Pseudobythopirellula and the novel species Bythopirellula polymerisocia and Posidoniimonas corsicana.

Eight novel strains of the phylum Planctomycetes were isolated from different aquatic habitats. Among these habitats were the hydrothermal vent system close to Panarea Island, a public beach at Mallorca Island, the shore of Costa Brava (Spain), and three sites with brackish water in the Baltic Sea. The genome sizes of the novel strains range from 4.33 to 6.29 Mb with DNA G+C contents between 52.8 and 66.7%. All strains are mesophilic (Topt 24-30 °C) and display generation times between 17 and 94 h. All eight isolates constitute novel species of either already described or novel genera within the family Lacipirellulaceae. Two of the novel species, Posidoniimonas polymericola (type strain Pla123aT = DSM 103020T = LMG 29466T) and Bythopirellula polymerisocia (type strain Pla144T = DSM 104841T = VKM B-3442T), belong to established genera, while the other strains represent the novel genera Aeoliella gen. nov., Botrimarina gen. nov., Pirellulimonas gen. nov. and Pseudobythopirellula gen. nov. Based on our polyphasic analysis, we propose the species Aeoliella mucimassa sp. nov. (type strain Pan181T = DSM 29370T = LMG 31346T = CECT 9840T = VKM B-3426T), Botrimarina colliarenosi sp. nov. (type strain Pla108T = DSM 103355T = LMG 29803T), Botrimarina hoheduenensis sp. nov. (type strain Pla111T = DSM 103485T = STH00945T, Jena Microbial Resource Collection JMRC), Botrimarina mediterranea sp. nov. (type strain Spa11T = DSM 100745T = LMG 31350T = CECT 9852T = VKM B-3431T), Pirellulimonas nuda sp. nov. (type strain Pla175T = DSM 109594T = CECT 9871T = VKM B-3448T) and Pseudobythopirellula maris sp. nov. (type strain Mal64T = DSM 100832T = LMG 29020T).

Stieleria varia sp. nov., isolated from wood particles in the Baltic Sea, constitutes a novel species in the family Pirellulaceae within the phylum Planctomycetes.

Species belonging to the bacterial phylum Planctomycetes are ubiquitous members of the microbial communities in aquatic environments and are frequently isolated from various biotic and abiotic surfaces in marine and limnic water bodies. Planctomycetes have large genomes of up to 12.4 Mb, follow complex lifestyles and display an uncommon cell biology; features which motivate the investigation of members of this phylum in greater detail. As a contribution to the current collection of axenic cultures of Planctomycetes, we here describe strain Pla52T isolated from wood particles in the Baltic Sea. Phylogenetic analysis places the strain in the family Pirellulaceae and suggests two species of the recently described genus Stieleria as current closest neighbours. Strain Pla52nT shows typical features of members of the class Planctomycetia, including division by polar budding and the presence of crateriform structures. Colonies of strain Pla52nT have a light orange colour, which is an unusual pigmentation compared to the majority of members in the phylum, which show either a pink to red pigmentation or entirely lack pigmentation. Optimal growth of strain Pla52nT at 33 °C and pH 7.5 indicates a mesophilic (i.e. with optimal growth between 20 and 45 °C) and neutrophilic growth profile. The strain is an aerobic heterotroph with motile daughter cells. Its genome has a size of 9.6 Mb and a G + C content of 56.0%. Polyphasic analyses justify delineation of the strain from described species within the genus Stieleria. Therefore, we conclude that strain Pla52nT = LMG 29463T = VKM B-3447T should be classified as the type strain of a novel species, for which we propose the name Stieleria varia sp. nov.

Caulifigura coniformis gen. nov., sp. nov., a novel member of the family Planctomycetaceae isolated from a red biofilm sampled in a hydrothermal area.

Pan44T, a novel strain belonging to the phylum Planctomycetes, was isolated from a red biofilm in a hydrothermal area close to the island Panarea in the Tyrrhenian Sea north of Sicily, Italy. The strain forms white colonies on solid medium and displays the following characteristics: cell division by budding, formation of rosettes, presence of matrix or fimbriae and long stalks. The cell surface has an interesting and characteristic texture made up of triangles and rectangles, which leads to a pine cone-like morphology of the strain. Strain Pan44T is mesophilic (temperature optimum 26 °C), slightly alkaliphilic (pH optimum 8.0), aerobic and heterotrophic. The strain has a genome size of 6.76 Mb with a G + C content of 63.2%. Phylogenetically, the strain is a member of the family Planctomycetaceae, order Planctomycetales, class Planctomycetia. Our analysis supports delineation of strain Pan44T from all known genera in this family, hence, we propose to assign it to a novel species within a novel genus, for which we propose the name Caulifigura coniformis gen. nov., sp. nov., represented by Pan44T (DSM 29405T = LMG 29788T) as the type strain.

Tautonia plasticadhaerens sp. nov., a novel species in the family Isosphaeraceae isolated from an alga in a hydrothermal area of the Eolian Archipelago.

A novel planctomycetal strain, designated ElPT, was isolated from an alga in the shallow hydrothermal vent system close to Panarea Island in the Tyrrhenian Sea. Cells of strain ElPT are spherical, form pink colonies and display typical planctomycetal characteristics including division by budding and presence of crateriform structures. Strain ElPT has a mesophilic (optimum at 30 °C) and neutrophilic (optimum at pH 7.5) growth profile, is aerobic and heterotrophic. It reaches a generation time of 29 h (µmax = 0.024 h-1). The strain has a genome size of 9.40 Mb with a G + C content of 71.1% and harbours five plasmids, the highest number observed in the phylum Planctomycetes thus far. Phylogenetically, the strain represents a novel species of the recently described genus Tautonia in the family Isosphaeraceae. A characteristic feature of the strain is its tendency to attach strongly to a range of plastic surfaces. We thus propose the name Tautonia plasticadhaerens sp. nov. for the novel species, represented by the type strain ElPT (DSM 101012T = LMG 29141T).

Aureliella helgolandensis gen. nov., sp. nov., a novel Planctomycete isolated from a jellyfish at the shore of the island Helgoland.

A novel planctomycetal strain, designated Q31aT, was isolated from a jellyfish at the shore of the island Helgoland in the North Sea. The strain forms lucid white colonies on solid medium and displays typical characteristics of planctomycetal strains, such as division by budding, formation of rosettes, presence of crateriform structures, extracellular matrix or fibre and a holdfast structure. Q31aT is mesophilic (temperature optimum 27 °C), neutrophilic (pH optimum 7.5), aerobic and heterotrophic. A maximal growth rate of 0.017 h- 1 (generation time of 41 h) was observed. Q31aT has a genome size of 8.44 Mb and a G + C content of 55.3%. Phylogenetically, the strain represents a novel genus and species in the recently introduced family Pirellulaceae, order Pirellulales, class Planctomycetia. We propose the name Aureliella helgolandensis gen. nov., sp. nov. for the novel species, represented by Q31aT (= DSM 103537T = LMG 29700T) as the type strain.

Data on enterobacteria activity on biofilm formation at surface mango fruit (Mangifera indica L.) cv Ataulfo.

Abiotic factors influenced the capacity of the strains to form biofilms. Classification of the adhesion type is related with the optical density measured on the biofilm formation of tested strains. The relationship between the biofilm formation in real values with theoretical values of the strains was used to determine the mechanism involved during mixed cultures.

Anti-adhesion activity of thyme (Thymus vulgaris L.) extract, thyme post-distillation waste, and olive (Olea europea L.) leaf extract against Campylobacter jejuni on polystyrene and intestine epithelial cells.

BACKGROUND: In order to survive in food-processing environments and cause disease, Campylobacter jejuni requires specific survival mechanisms, such as biofilms, which contribute to its transmission through the food chain to the human host and present a critical form of resistance to a wide variety of antimicrobials. RESULTS: Phytochemical analysis of thyme ethanolic extract (TE), thyme post-hydrodistillation residue (TE-R), and olive leaf extract (OE) using high-performance liquid chromatography with photodiode array indicates that the major compounds in TE and TE-R are flavone glucuronides and rosmarinic acid derivatives, and in OE verbascoside, luteolin 7-O-glucoside and oleuroside. TE and TE-R reduced C. jejuni adhesion to abiotic surfaces by up to 30% at 0.2-12.5 µg mL(-1) , with TE-R showing a greater effect. OE from 3.125 to 200 µg mL(-1) reduced C. jejuni adhesion to polystyrene by 10-23%. On the other hand, C. jejuni adhesion to PSI cl1 cells was inhibited by almost 30% over a large concentration range of these extracts. CONCLUSION: Our findings suggest that TE, the agro-food waste material TE-R, and the by-product OE represent sources of bioactive phytochemicals that are effective at low concentrations and can be used as therapeutic agents to prevent bacterial adhesion. © 2015 Society of Chemical Industry.