Biology subjects

Nesporova, K.

Publications and source records attributed to Nesporova, K..

8 recordsLinked to original sources

bioRxiv2026

Characterization of a chronic UV-induced photoaging mouse model: insights into skin barrier dysfunction, extracellular matrix remodeling, and altered adipogenesis

Chronic exposure to ultraviolet (UV) radiation, known as photoaging, accelerates skin aging by inducing molecular, histological, and functional changes. This study established a mouse model using SKH-1 hairless mice to investigate chronic UV-induced photoaging over eight weeks. SKH-1 hairless mice were exposed to a combination of UVA and UVB, and the progression of skin damage was monitored through physical, histological, and molecular parameters, with a focus on erythema, transepidermal water loss, and collagen and hyaluronan (HA) metabolism. Significant reductions in HA content and alterations in DNA repair markers, such as {gamma}H2AX, were observed, highlighting the impact of chronic UV exposure on skin structure and function. Reactive adipogenesis and increased epidermal thickness were noted, reflecting adaptive responses to UV-induced damage. By investigating these parameters over the evaluation period, we provide a comprehensive time-course analysis of the progressive impact of UV-induced photoaging, offering insights into the underlying mechanisms and potential therapeutic targets to prevent or delay photoaging.

pathology↗

bioRxiv2026

Macrophage-based assays for the in vitro testing of the anti-inflammatory activity of mesenchymal stem cell-based products

Therapies based on mesenchymal stromal cells (MSCs) have high potential in the field of regenerative medicine due mainly to their immunomodulatory properties. However, their clinical translation is hampered by a lack of sufficiently standardised potency tests. Since macrophages comprise key mediators of the effects of MSCs, macrophage-based assays potentially provide a relevant in vitro tool for the evaluation of the activity of MSC products. This study involved the coculturing of canine adipose-derived mesenchymal stem cells (ASCs) with macrophages derived from human THP-1 and U937 monocyte cell lines, murine RAW264.7 macrophages and primary human macrophages. The M2 polarisation was assessed following stimulation with IL-4/IL-13. The mRNA expression of the pro- and anti-inflammatory markers was analysed applying qPCR. The ASC secretome acted to reduce the pro-inflammatory mRNA expression across all the macrophage models, albeit with a certain degree of model-dependent variability. Only the U937 macrophages responded consistently to the M2-polarising stimuli, while the RAW264.7 cells provided practical advantages in terms of routine screening. The results thus provided support for the application of macrophage-based potency assays as a suitable platform for the testing of MSC products; the U937 cells were found to be particularly suitable for the study of polarisation and the RAW264.7 cells for standardised screening.

cell biology↗

bioRxiv2025

From ecology to evolution: plasmid- and colicin-mediated persistence of antibiotic resistant Escherichia coli in gulls

Antimicrobial resistance in wildlife is an emerging concern within the One Health concept. Gulls, due to their synanthropic behaviour and long-distance migration, are recognised as vectors and secondary reservoirs of resistant bacteria. These birds can facilitate the environmental spread of resistant strains across ecosystem boundaries. Understanding their role in shaping microbial communities is essential for assessing the broader ecological impact. This study investigates the persistence and competitive dynamics of cephalosporin-resistant Escherichia coli in Caspian gulls captured at their breeding colony at a water reservoir and subsequently monitored in captivity for three months, representing the longest in vivo experiment of its kind conducted on wild birds. We observed sustained colonization and long-term shedding of resistant E. coli throughout the entire study, marking the longest documented carriage of resistant bacteria in wild birds to date. Notably, rapid dissemination of various E. coli sequence types (STs) with CTX-M-1 was observed, with ST11138 rapidly outcompeting other strains, including the initially dominant ST11893. Genomic analyses revealed that ST11138 harboured F24:A-:B1 and IncI1/ST3/CTX-M-1 plasmids encoding colicins and corresponding immunity genes, likely conferring a competitive advantage. Our findings underscore the role of bacteriocin-mediated interactions in shaping microbial communities and highlight the importance of plasmid-encoded traits in the persistence of resistant strains in wildlife. Importantly, our findings underscore the ecological novelty of longitudinal in vivo tracking of AMR persistence in natural hosts and highlight the need to consider ecological and microbiome-level interactions when assessing the environmental dimension of AMR under the One Health concept. ImportanceAntimicrobial resistance in wildlife is an emerging concern within the One Health framework, with gulls recognized as important vectors and secondary reservoirs of resistant bacteria. Due to their synanthropic behaviour and long-distance migration, these birds can facilitate the spread of resistant strains across ecosystems. However, the role of wildlife in resistance dynamics remains underexplored, especially in long-term, natural settings. Our study is unique in its scope and duration, representing the longest in vivo experiment of its kind conducted on wild birds. By capturing these processes in live hosts under naturalistic conditions and across an extended period, our study provides rare and ecologically grounded insights into how antimicrobial resistance is maintained outside clinical or laboratory settings. Our findings show sustained colonization and long-term shedding of resistant E. coli, with strain ST11138 outcompeting others. Genomic analyses reveal plasmid-encoded traits, highlighting the novel ecological and evolutionary mechanisms underlying resistance maintenance in wildlife.

microbiology↗

bioRxiv2025

The absence of the ompA and type VI secretion system in the successful lineage of Acinetobacter baumannii ST19

Acinetobacter baumannii is an opportunistic pathogen, often multi- to pandrug-resistant, including to last-resort antibiotics such as carbapenems. A. baumannii can acquire DNA through multiple mechanisms including natural competence and conjugation. An active Type VI Secretion System (T6SS), which kills nonkin bacteria and challenges and inhibits the conjugation. The acquisition of resistance genes has helped the spread of resistant clones of A. baumannii, such as those of Sequence Types (STPas), ST1, ST2, ST10, ST15, ST25, ST79 and ST85. While ST1 and ST2 were thoroughly studied, there are new emerging clones whose genetic background facilitating the rise is still unknown or poorly understood. The emergence of Acinetobacter baumannii ST19 first peaked in 2003, coinciding with the Iraq conflict and increased detection among U.S. military personnel. Its prevalence later surged in Georgia and Ukraine, around the onset of the conflict in Ukraine in 2022, associating it with regions affected by military activity. In this study, we have sequenced whole-genome three isolates of A. baumannii ST19 and compared them with further 156 A. baumannii ST19 genomes were obtained from public repositories. In total, 157/159 genomes revealed loss of T6SS locus, which was replaced in 56/157 genomes (35,7%) by {Delta}Tn9 carrying chloramphenicol and {Delta}Tn10 carrying tetracycline resistance genes, and formaldehyde and chlorite resistance genes. Surprisingly, the antibiotic resistance-encoding transposons likely originated from Enterobacteriaceae plasmids. The loss of a functional T6SS in A. baumannii ST19 may potentially facilitate horizontal gene transfer and promoting a cooperative or less competitive lifestyle providing a selective advantage at the population level.

microbiology↗

bioRxiv2025

Complex interplay between gene deletions and the environment uncovers cellular roles for genes of unknown function in Escherichia coli

Phenotypic outcomes can be heavily affected by environmental factors. In this study, we exploited the previously observed nutrient-dependency of cell biological phenotypic features, captured by a cross-condition image-based profiling assay of Escherichia coli deletion strains, to examine this in more detail. We identified several general principles, including the existence of a spectrum of deviating phenotypes across nutrient conditions (i.e., from nutrient- or feature-specific to pleiotropic phenotypic deviations), limited conservation of phenotypic deviations across nutrient conditions (i.e., limited phenotypic robustness), and a subset of nutrient-independent phenotypic deviations (indicative of consistent genetic determinants of specific phenotypic features). In a subsequent step, we used this cross-condition dataset to identify five genes of unknown function of which the deletion displayed either nutrient-independent phenotypic deviations or phenotypic similarities to genes of known function: yibN, yaaY, yfaQ, ybiJ, and yijD. These genes showed different levels of phylogenetic conservation, ranging from conserved across the tree of life (yibN) to only present in some genera of the Enterobacterales (yaaY). Analysis of the structural properties of the proteins encoded by these y-genes, identification of structural similarities to other proteins, and the examination of their subcellular localization yielded new insights into their contribution to E. coli cell morphogenesis, cell cycle progression and cell growth. Together, our approach showcases how bacterial image-based profiling assays and datasets can serve as a gateway to reveal the function of uncharacterized proteins. ImportanceDespite unprecedented access to genomic information, predicting phenotypes based on genotypes remains notoriously difficult. One major confounding factor is the environment and its ability to modulate phenotypic outcomes. Another is the fact that a large fraction of protein-coding genes in bacterial genomes remains uncharacterized and have no known function. In this work, we use a large-scale cross-condition image-based profiling dataset to characterize nutrient-dependent phenotypic variability of E. coli deletion strains and exploit it to provide insight into the cellular role of genes of unknown function. Through our analysis, we identified five genes of unknown function that we subsequently further characterized by examining their phylogenetic conservation, predicted structural properties and similarities, and their intracellular localization. Combined, this approach highlights the potential of cross-condition image-based profiling, which extracts many cell biological phenotypic readouts across multiple conditions, to better understand nutrient-dependent phenotypic variability and uncover protein function.

microbiology↗

bioRxiv2025

Large-scale genomic analysis reveals the distribution and diversity of Type VI Secretion Systems in Escherichia coli

The type VI secretion system (T6SS) is a versatile nanomachine that injects effectors into target cells, playing a role in bacterial competition and virulence. While widespread in Gram-negative bacteria, T6SS prevalence varies across species and strains, and its distribution in Escherichia coli remains underexplored despite E. coli being an important intestinal (IPEC) and extraintestinal (ExPEC) pathogen. Here, we examined the prevalence and distribution of T6SS subclasses (T6SSi) across 131610 E. coli genomes, which we annotated for clinical relevance. T6SS genes were identified while focusing on the three subclasses of T6SSi gene clusters known to be present in E. coli: T6SSi1, T6SSi2, and T6SSi4b. Across phylogenetic groups, T6SSi1 was broadly present, while T6SSi2 showed associations with B1, B2, and G, and T6SSi4b was rare. T6SSi1 was primarily associated with IPEC, and T6SSi2 with ExPEC. Even clearer patterns emerged at the sequence type (ST) level or when strains were further categorized into pathovars. For example, both the most dominant ExPEC and IPEC ST (ST131 and ST11, respectively) displayed niche-specific T6SS trends, with non-complete T6SSs being more associated with humans. In a final step, we evaluated the co-occurrence of T6SSs with other virulence-associated genes (VAGs) and multidrug resistance (MDR). This analysis confirmed the association of T6SSi1 and T6SSi2 with IPEC- and ExPEC-associated VAGs, respectively, and revealed a negative correlation between complete T6SSi subclasses and MDR. Together, our work provides a comprehensive overview of the diversity of T6SSs across E. coli, shedding more light on their potential contribution to pathogenicity in this species. ImportanceOur study represents a large-scale analysis of T6SSs across one of the most comprehensive collections of E. coli genomes to date. In doing so, we updated several misconceptions on T6SSs distribution and other genomic properties of E. coli strains, which originated from smaller scale studies and were subsequently extrapolated in the literature. This includes the prevalence and distribution of T6SSi subclasses across phylogenetic groups (e.g., T6SS i2 is not prevalent in phylogroup D), the association of specific virulence factors with IPEC and/or ExPEC (e.g., hemolysin A is more often associated with IPEC and not a typical ExPEC characteristic), and characteristics of pathogenic STs (e.g., ST131 displays distinct genomic properties based on its environmental niche). As such, this study not only advances our understanding of T6SS in E. coli, but also serves as a valuable resource for future studies on the clinical relevance and distribution of other genetic elements.

microbiology↗

bioRxiv2023

Plasmid-mediated colistin resistance among human clinical Enterobacterales isolates: National surveillance in the Czech Republic

The occurrence of colistin resistance has increased rapidly among Enterobacterales around the world. We performed a national survey of plasmid-mediated colistin resistance in human clinical isolates by a retrospective analysis of samples from 2009-2017 and a prospective sampling in 2018-2020. The aim of this study was to identify and characterize isolates with mcr genes from various regions of the Czech Republic using whole genome sequencing (WGS). Of all 1932 colistin-resistant isolates analyzed, 73 (3.8%) were positive for mcr genes. Most isolates carried mcr-1 (48/73) and were identified as Escherichia coli (n=44) and Klebsiella pneumoniae (n=4) of various sequence types (ST). Twenty-five isolates including Enterobacter spp. (n=24) and Citrobacter freundii (n=1) carrying mcr-9 gene were detected, three of them (Enterobacter kobei ST54) co-harbored the mcr-4 and mcr-9 genes. Multi-drug resistance phenotype was a common feature of mcr isolates and 14% (10/73) isolates also co-harboured clinically important beta-lactamases including 2 isolates with carbapenemases KPC-2 and OXA-48. Phylogenetic analysis of E. coli ST744, the dominant genotype in this study, with the global collection, showed Czech isolates belonged to two major clades, one containing isolates from Europe, while the second composed of isolates from diverse geographical areas. The mcr-1 gene was carried by IncX4 (34/73, 47%), IncHI2/ST4 (6/73, 8%) and IncI2 (8/73, 11%) plasmid groups. Small plasmids belonging to the ColE10 group were associated with mcr-4 in three isolates while mcr-9 was carried by IncHI2/ST1 plasmids (4/73, 5%) or the chromosome (18/73, 25%). We showed an overall low level of occurrence of mcr genes in colistin-resistant bacteria from human clinical samples in the Czech Republic.

microbiology↗

bioRxiv2022

What are the reference strains of Acinetobacter baumannii referring to?

We assembled the whole genome sequence (WGS) of a collection of 43 non-redundant modern clinical isolates and four broadly used reference strains of Acinetobacter baumannii. Comparison of these isolates and their WGS confirmed the high heterogeneity in capsule loci, sequence types, the presence of virulence and antibiotic resistance genes. However, a significant portion of clinical isolates strongly differ when compared to several reference strains in the light of colony morphology, cellular density, capsule production, natural transformability and in vivo virulence. These genetic and phenotypic differences between current circulating strains of A. baumannii and established reference strains could hamper the study of A. baumannii as an entity. The broadly used reference strains led to the current state of the art of the A. baumannii field, however, we propose that established reference strains in the A. baumannii field should be carefully used, because of the high genetic and phenotypic heterogeneities. In this study, we generated a collection of high-quality nucleotide sequences of 43 modern clinical isolates with the corresponding multi-level phenotypic characterizations. Beside the contribution of novel fundamental observations generated in this study, the phenotypic and genetic data, along with the bacterial strains themselves, will be further accessible using the first open access online platform called "Acinetobase". Therefore, a rational choice of modern strains will be possible to select the ones that suit the needs of specific biological questions.

microbiology↗