1. Determinants of diarrhea, phenotypic and genomic characterization of Escherichia coli isolates from diarrheic and non-diarrheic patients attending public primary health facilities in Addis Ababa and Hossana, Ethiopia : dissertationWolde Deneke, 2025, doktorska disertacija Ključne besede: dissertations, Escherichia coli, antimicrobial resistance, genetic diversity, antimicrobial resistance genes, virulence-associated genes, mobile genetic elements, phylogenetic groups, whole-genome sequencing
Objavljeno v DKUM: 10.04.2025; Ogledov: 0; Prenosov: 27
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2. Ribotype classification of Clostridioides difficile isolates Is not predictive of the amino acid sequence diversity of the toxin virulence factors TcdA and TcdBZhenghui Li, Kwok Lee, Urvi Rajyaguru, C. Hal Jones, Sandra Janežič, Maja Rupnik, Annaliesa S. Anderson, Paul Liberator, 2020, izvirni znanstveni članek Opis: Clostridioides (Clostridium) difficile is the most commonly recognized cause of infectious diarrhea in healthcare settings. Currently there is no vaccine to prevent initial or recurrent C. difficile infection (CDI). Two large clostridial toxins, TcdA and TcdB, are the primary virulence factors for CDI. Immunological approaches to prevent CDI include antibody-mediated neutralization of the cytotoxicity of these toxins. An understanding of the sequence diversity of the two toxins expressed by disease causing isolates is critical for the interpretation of the immune response to the toxins. In this study, we determined the whole genome sequence (WGS) of 478 C. difficile isolates collected in 12 countries between 2004 and 2018 to probe toxin variant diversity. A total of 44 unique TcdA variants and 37 unique TcdB variants were identified. The amino acid sequence conservation among the TcdA variants (>98%) is considerably greater than among the TcdB variants (as low as 86.1%), suggesting that different selection pressures may have contributed to the evolution of the two toxins. Phylogenomic analysis of the WGS data demonstrate that isolates grouped together based on ribotype or MLST code for multiple different toxin variants. These findings illustrate the importance of determining not only the ribotype but also the toxin sequence when evaluating strain coverage using vaccine strategies that target these virulence factors. We recommend that toxin variant type and sequence type (ST), be used together with ribotype data to provide a more comprehensive strain classification scheme for C. difficile surveillance during vaccine development objectives.
Ključne besede: Clostridioides difficile, Clostridium difficile, TCDB, TcdA, vaccines, whole genome sequencing
Objavljeno v DKUM: 28.01.2025; Ogledov: 0; Prenosov: 10
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3. Why? - Successful Pseudomonas aeruginosa clones with a focus on clone CChanghan Lee, Jens Klockgether, Sebastian Fischer, Janja Trček, Burkhard Tümmler, Ute Römling, 2020, pregledni znanstveni članek Opis: The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.
Ključne besede: disaggregase, FtsH, genomic island, protein homeostasis, pulsed field gel electrophoresis, whole genome sequencing
Objavljeno v DKUM: 28.01.2025; Ogledov: 0; Prenosov: 5
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4. Comparison of microbial populations in saliva and feces from healthy and celiac adolescents with conventional and molecular approaches after cultivation on gluten-containing media : an exploratory studyTilen Seničar, Andraž Kukovičič, Valerija Tkalec, Aleksander Mahnič, Jernej Dolinšek, Maja Rupnik, 2021, izvirni znanstveni članek Opis: Microbes capable of metabolizing gluten are common in various parts of the intestinal tract. In this study, saliva and fecal samples were obtained from 10 adolescents (13-18 years of age), five of which had celiac disease (CD) and five of which were healthy volunteers (HV). Culture-enriched saliva and fecal samples were compared with molecular profiling, and microorganisms displaying lysis zones on gluten-containing media (i.e., gluten-degrading microorganisms; GDMs) were isolated. In total, 45 gluten-degrading strains were isolated, belonging to 13 genera and 15 species, including Candida albicans and Veillonella. GDMs were more common in HVs compared to CD patients and more diverse in saliva compared to feces. In saliva, GDMs showed partial overlap between HVs and CD patients. Bacterial communities in fecal samples determined with amplicon sequencing significantly differed between CD patients and HVs. Overall, 7-46 of all operational taxonomic units (OTUs) per sample were below the detection limit in the fecal samples but were present in the cultivated samples, and mainly included representatives from Lactobacillus and Enterococcus. Furthermore, differences in fecal short-chain fatty-acid concentrations between CD patients and HVs, as well as their correlations with bacterial taxa, were demonstrated.
Ključne besede: gluten-degrading microorganisms, veillonella, candida, short-chain fatty acids, celiac disease, microbiota, sequencing
Objavljeno v DKUM: 14.10.2024; Ogledov: 0; Prenosov: 18
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5. Adipose tissue gene expression of entire male, immunocastrated and surgically castrated pigsKlavdija Poklukar Žnidaršič, Marjeta Čandek-Potokar, Milka Vrecl, Nina Batorek Lukač, Gregor Fazarinc, Kevin Kress, Volker Stefanski, Martin Škrlep, 2021, izvirni znanstveni članek Opis: Differences in adipose tissue deposition and properties between pig male sex categories, i.e., entire males (EM), immunocastrates (IC) and surgical castrates (SC) are relatively well-characterized, whereas the underlying molecular mechanisms are still not fully understood. To gain knowledge about the genetic regulation of the differences in adipose tissue deposition, two different approaches were used: RNA-sequencing and candidate gene expression by quantitative PCR. A total of 83 differentially expressed genes were identified between EM and IC, 15 between IC and SC and 48 between EM and SC by RNA-sequencing of the subcutaneous adipose tissue. Comparing EM with IC or SC, upregulated genes related to extracellular matrix dynamics and adipogenesis, and downregulated genes involved in the control of lipid and carbohydrate metabolism were detected. Differential gene expression generally indicated high similarity between IC and SC as opposed to EM, except for several heat shock protein genes that were upregulated in EM and IC compared with SC. The candidate gene expression approach showed that genes involved in lipogenesis were downregulated in EM compared with IC pigs, further confirming RNA-sequencing results.
Ključne besede: pigs, adipose tissue, entire males, immunocastration, surgical castration, RNA-sequencing, expression
Objavljeno v DKUM: 10.10.2024; Ogledov: 0; Prenosov: 5
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7. Določanje sekvence DNK na osnovi Eulerjeve poti z uporabo izboljšanega Hierholzerjevega algoritma : magistrsko deloFilip Mesarić, 2019, magistrsko delo Opis: In the master’s thesis we created the algorithm for DNA sequencing based on an Eulerian path
and the improved Hierholzer’s algorithm. The theoretical part explains the graph theory,
existing Eulerian path searching algorithms and Hierholzer's algorithmic implementations.
Additionally, the theoretical part presents DNA sequencing and its most popular methods. The
practical part focuses on the development of an application that shows DNA sequencing based
on an Eulerian path and the improved Hierholzer's algorithm. The results represent an
improvement of sequencing, taking into consideration time and distance measurements, for
our implementation in comparison with the existing Hierholzer’s algorithm.
Ključne besede: DNA, Eulerian path, Hierholzer’s algorithm, DNA sequencing
Objavljeno v DKUM: 15.07.2019; Ogledov: 1335; Prenosov: 114
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8. Effect of Bifidobacterium breve on the intestinal microbiota of coeliac children on gluten free diet : a pilot studyAndrea Quagliariello, Irene Aloisio, Nicole Bozzi Cionci, Donata Luiselli, Giuseppe D'Auria, Llúcia Martinez-Priego, David Pérez-Villarroya, Tomaž Langerholc, Maša Kozmos, Dušanka Mičetić-Turk, Diana Di Gioia, 2016, izvirni znanstveni članek Opis: Coeliac disease (CD) is associated with alterations of the intestinal microbiota. Although several Bifidobacterium strains showed anti-inflammatory activity and prevention of toxic gliadin peptides generation in vitro, few data are available on their efficacy when administered to CD subjects. This study evaluated the effect of administration for three months of a food supplement based on two Bifidobacterium breve strains (B632 and BR03) to restore the gut microbial balance in coeliac children on a gluten free diet (GFD). Microbial DNA was extracted from faeces of 40 coeliac children before and after probiotic or placebo administration and 16 healthy children (Control group). Sequencing of the amplified V3-V4 hypervariable region of 16S rRNA gene as well as qPCR of Bidobacterium spp., Lactobacillus spp., Bacteroides fragilis group Clostridium sensu stricto and enterobacteria were performed. The comparison between CD subjects and Control group revealed an alteration in the intestinal microbial composition of coeliacs mainly characterized by a reduction of the Firmicutes/Bacteroidetes ratio, of Actinobacteria and Euryarchaeota. Regarding the effects of the probiotic, an increase of Actinobacteria was found as well as a re-establishment of the physiological Firmicutes/Bacteroidetes ratio. Therefore, a three-month administration of B. breve strains helps in restoring the healthy percentage of main microbial components.
Ključne besede: coeliac disease, gluten free diet, probiotic, Bifidobacterium breve, intestinal microbiota, qPCR, next generation sequencing
Objavljeno v DKUM: 22.06.2017; Ogledov: 2591; Prenosov: 287
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