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Abstract: Iron uptake plays an important role in the persistence of Escherichia coli in the host and for its survival in the environment, and it is known that E. coli has a variety of siderophore systems for iron uptake. We investigated the ability to produce siderophores, the genetic diversity of the siderophores and their correlation with virulence-associated genes (VAGs), phylogroups and bacteriocin production in E. coli strains isolated from different sources: uropathogenic E. coli (UPEC) from urine of patients with urinary tract infections, avian pathogenic E. coli (APEC) from organs of birds with signs of colibacillosis, fecal E. coli (FEC) from feces of healthy cattle and E. coli from organic fertilizers based on poultry and cattle manure (OFEC). A high variability in siderophore production was found among the UPEC strains studied, while the OFEC strains showed the highest siderophore production among all groups. Genes for aerobactin and yersiniabactin receptors were most frequently found in the UPEC strain, followed by the APEC, FEC and OFEC strains. The greatest diversity of siderophore receptors was found in the APEC strain. We also found that iutA-positive E. coli isolated from animals contained more VAGs than iutA-negative strains. The profiles of the siderophore genes of APEC and OFEC from poultry manure were very similar, indicating that APEC can be transmitted via organic fertilizers, suggesting that poultry manure is an environmental risk. The data obtained complement the information on the prevalence of siderophore producers and contribute to our knowledge on the biodiversity of E. coli pathotypes.
Keywords: siderophore, Escherichia coli, virulence-associated genes, phylogenetic group, bacteriocin, microcin
Published in DKUM: 18.07.2025; Views: 0; Downloads: 1
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Abstract: Autism spectrum disorders (ASD) represent a phenotypically heterogeneous group of patients that strongly intertwine with other neurodevelopmental disorders (NDDs), with genetics playing a significant role in their etiology. Whole exome sequencing (WES) has become predominant in molecular diagnostics for ASD by considerably increasing the diagnostic yield. However, the proportion of undiagnosed patients still remains high due to complex clinical presentation, reduced penetrance, and lack of segregation analysis or clinical information. Thus, reverse phenotyping, where we first identified a possible genetic cause and then determine its clinical relevance, has been shown to be a more efficient approach. WES was performed on 147 Slovenian pediatric patients with suspected ASD. Data analysis was focused on identifying ultrarare or “single event” variants in ASD-associated genes and further expanded to NDD-associated genes. Protein function and gene prioritization were performed on detected clinically relevant variants to determine their role in ASD etiology and phenotype. Reverse phenotyping revealed a pathogenic or likely pathogenic variant in ASD-associated genes in 20.4% of patients, with subsequent segregation analysis indicating that 14 were de novo variants and 1 was presumed compound heterozygous. The diagnostic yield was further increased by 2.7% by the analysis of ultrarare or “single event” variants in all NDD-associated genes. Protein function analysis established that genes in which variants of unknown significance (VUS) were detected were predominantly the cause of intellectual disability (ID), and in most cases, features of ASD as well. Using such an approach, variants in rarely described ASD-associated genes, such as SIN3B, NR4A2, and GRIA1, were detected. By expanding the analysis to include functionally similar NDD genes, variants in KCNK9, GNE, and other genes were identified. These would probably have been missed by classic genotype–phenotype analysis. Our study thus demonstrates that in patients with ASD, analysis of ultrarare or “single event” variants obtained using WES with the inclusion of functionally similar genes and reverse phenotyping obtained a higher diagnostic yield despite limited clinical data. The present study also demonstrates that most of the causative genes in our cohort were involved in the syndromic form of ASD and confirms their comorbidity with other developmental disorders.
Keywords: reverse phenotyping, single event variants, NDD-associated genes, GRIA1 gene, NR4A2 gene, SIN3B gene, autism, child
Published in DKUM: 12.12.2024; Views: 0; Downloads: 8
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Keywords: colorectal cancer, tumour suppressor genes DCN
Published in DKUM: 05.06.2012; Views: 2073; Downloads: 171
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