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Avian pathogenic E. coli (APEC), produces an extraintestinal infection in chickens, turkeys, and other types of birds, called colibacillosis, which is considered one of the main causes of economic losses due to morbidity, mortality, and discard of poultry carcasses. The objective of the present study was to characterize the genetic profile of the virulence factors of different isolates of avian E. coli in Caloto, Cauca, Colombia. Materials and methods: E. coli was isolated and identified by biochemical tests, from 47 clinical isolates. Subsequently, the DNA was extracted using Chelex. Three multiplex PCRs were designed to amplify 13 virulence factors (iroN, hlyF, iss, iutA, frz, vat, sitA, KpsM, sitD, fimH, pstB, sopB, and uvrY), using primers previously reported for each. At the end, the amplification products were verified on agarose gels. Each isolate was classified according to the number of virulence factors: group A (between 10 and 13), group B (between 5 and 9), and group C (4 or less). Discussion and Conclusions: we were able to identify the presence of a group of virulence factors in clinical isolates of APEC, which allows us to demonstrate that both the frequency and the profile of virulence factors in the isolated strains showed a different profile than the reported by other authors. The virulence genes pstB and fimH were detected in all our samples, and the iss gene was the one with the lowest frequency. Finally, according to the number of virulence factors, the group A was the most frequent.

Background & objectives: Trypanosoma cruzi and Leishmania spp. are protozoans that cause American trypanosomiasis and leishmaniasis, respectively. In endemic foci where both diseases coincide, coinfection can occur. The objective of this work was the characterization of the parasites involved in coinfection in several endemic areas of Venezuela. Methods: Molecular characterization was done in 30 samples of several species of mammals (Didelphis marsupialis, Equus mulus, Rattus rattus, Canis familiaris, Felis catus, and Sciurus granatensis) from the states of Anzoategui, Cojedes and Capital District diagnosed with T. cruzi and Leishmania spp. coinfections. For the typing of T. cruzi DTUs, the markers of miniexon, 24Sa rDNA, 18Sa rDNA, and hsp60-PCR-RFLP (EcoRV) were used. Infection by Leishmania spp. was characterized by miniexon multiplex PCR for complexes of Leishmania and ITS1-PCR-RFLP (HaeIII, HhaI, and RsaI) for the identification of the species. Results: The T. cruzi TcI was present in 100% of the coinfected mammals, which included 76.7% of triple infection by T. cruzi TcI-complex-L. (L) mexicana-L. infantum/chagasi, 13.3% of double infection by T. cruzi TcI-L. mexicana and 10% of double infection by T. cruzi Tcl-L. infantum/chagasi. Interpretation & conclusion: These results suggest that the double or triple infection is a phenomenon existing in almost all the coendemics areas and mammals studied, which might influence the mechanisms of adaptation and pathogenicity of these parasites.

Background & objectives: For detection and molecular characterization of Babesia microti in laboratory mice from India. Methods: A total of 625 mice were screened by peripheral blood smear examination and subsequently was confirmed by PCR using a piroplasm conserved primer set (Piro A/B). Nested PCR was done using a species-specific primer targeting the gene encoding the small subunit ribosomal RNA (18S rRNA). The PCR products were cloned, purified and sequenced. A total of 12 isolates were obtained. The sequences were aligned and phylogenetic trees were prepared with other published Babesia spp. sequences. Results: B. microti was detected with a total infection rate of 8.80%. The higher rate of infection was observed by species specific PCR (8.80%) than examined by blood smear (7.20%). Sequence and phylogenetic analysis showed that Babesia species detected in mice were genetically identical to the genotypes of B. microti and can be easily distinguished from other genotypes of Babesia parasites by neighbour joining and maximum likelihood method. Intra-species analysis indicated that all the twelve isolates from six North-Eastern states of India have a close identity but inter-species showed genetic reservoir host for transmission of babesial infection to humans. Interpretation & conclusion: The detection of Babesia microti may suggest that laboratory mice may serve as potential reservoir host for human infection and possibility of innovative way of diagnosing and control of human babesiosis.

Porcine epidemic diarrhea virus (PEDV) is a major cause of devastating economic losses in the global swine industry. Sichuan Province, a major swine-producing region in China, is therefore a critical area for monitoring PEDV prevalence and evolution. We analyzed clinical samples collected from 365 diarrheic piglets across 70 pig farms located in 20 regions of Sichuan Province, China, from 2023 to 2024. The overall PEDV positivity rate was 40.27% (147/365). Prevalence varied considerably among regions, ranging from 0 to 63.64%, with over half (16/20) exceeding a 30% positivity rate, indicating widespread but heterogeneous circulation. Phylogenetic analyses based on the S gene from 33 representative strains revealed that they clustered into the G2b, G1c, and G2a subtypes, and these 33 PEDV S genes exhibited 94.3–99.9% nucleotide and 93.2–99.8% amino acid homology. The prevalent strains harbored frequent mutations in key antigenic sites of the S gene, including S10, SS6, and the collagenase equivalent (COE) domain. This study provides novel insights into the current epidemiology and genetic evolution of PEDV in China, which will inform more effective prevention and control strategies. Therefore, the control of the predominant G2b subtype should not be overlooked.

In this study, we performed a genetic diversity analysis using RAPD markers for some Vitex agnus-castus populations grown in Aydin, Turkey. Total genomic DNA isolation from the leaves of Vitex agnus-castus was performed using a commercial kit. Seven RAPD primers (OPA-02, OPA-05, OPA-13, OPA-15, OPA-16, OPA-18, OPA-20) were used to determine genetic diversity among populations. Polymerase Chain Reaction (PCR) was performed with all genomic DNA samples and primers. PCR products were run in agarose gel electrophoresis and visualized under UV light. The amplified products were scored as bands (1) and no bands (0) for all gel images and their matrix files were generated. A total of 36 characters were obtained from the primers. Phylogenetic relationships and genetic distances between the cultivars were calculated by using the PAUP* (Phylogenetic Analysis Using Parsimony and other methods) program. According to PAUP analysis, the closest genetic distances were between Çine pink flower and Çakmar purple flower, and Çakmar pink flower and Çakmar purple flower populations with a value of 0.05556; and the greatest genetic distance was between Çakmar pink flower and Köşk purple flower populations with a value of 0.36111. In the phylogenetic analysis obtained using UPGMA algorithms, the phylogenetic tree consisted of four groups. The results suggest that RAPD markers are useful tools for determining genetic relationships among Vitex agnus-castus genotypes.

Fig viruses are major challenges for fig production, and may be widely present in Croatia. A survey was carried out to determine the most economically important viruses of fig trees in the South Croatian Adriatic Region, by analyzing 28 fig genotypes from field sites and a national fig collection. Using RT-PCR and specific primers, five viruses were detected, including: fig badnavirus 1 (FBV-1) in all the assessed samples, fig mosaic virus (FMV) (55% of samples), fig leaf mottle-associated virus 1 (FLMaV-1) (44%), fig fleck-associated virus (FFkaV) (17%), and fig mild mottle-associated virus (FMMaV) (10% of samples). Most of the sampled trees were infected by multiple viruses, and only five harbored only FBV-1. Sequencing and phylogenetic analyses of two representative sequences for each of these viruses confirmed their identities and showed close relationships with Mediterranean isolates, indicating their regional dissemination. This study has provided new information of fig virus presence in the South Croatian Adriatic Region, is the first to report prevalence of FLMaV-1, FMMaV and FFkaV in Croatian fig germplasm, and to determine virus phylogenetic relationships. Virus monitoring in fig plantations and in certified propagation material, and integrated disease management strategies, are required to protect fig production in Croatia.

IntroductionAstroblastoma is a rare tumour of the central nervous system that often manifests with non-specific clinical symptoms and lacks distinct histological features. There is a pressing need for further understanding of the clinicopathological and molecular characteristics of Astroblastoma. Identifying mutant genes can aid in reliable and early diagnosis, as well as provide insights for the development of targeted therapies.MethodsThis study aims to investigate the clinicopathologic and molecular characteristics of astroblastoma. A total of four patients diagnosed with astroblastoma were included in the analysis. Clinical features, histological findings, and immunohistochemistry results were reviewed and analyzed. Genetic alterations were identified using fluorescence in situ hybridization (FISH) and next-generation sequencing (NGS), followed by patient follow-up.ResultsThe study included four female patients, ranging in age from 8 to 44 years. One patient had a tumour in the right parietal lobe, while the other three had tumours in the spinal cord. Histology is usually characterized by pseudorosettes of astroblasts and hyalinization of blood vessels. These tumors showed a growth pattern similar to traditional intracranial astroblastoma, and the histological manifestations of the four patients were all high-grade, showing features of high-density areas of tumor cells or necrosis. Immunohistochemical staining revealed that all four patients expressed OLIG2, EMA, and vimentin, while three patients also expressed GFAP and S-100. The Ki-67 positivity index was approximately 15% in three cases and 10% in one case. Fluorescence in situ hybridization (FISH) using break-apart probes showed EWRS1 breaks in three patients and MN1 breaks in one. Further DNA or RNA-targeted biallelic sequencing identified an EWSR1(Exon1-7)-BEND2(Exon2-14) fusion in case 1, and an EWSR1(Exon1-7)-BEND2(Intergenic) fusion in case 2. In case 3, an EWSR1(Exon1-7)-NUDT10(Intergenic) fusion was present, and in case 4, an MN1(Exon1)-BEND2(Exon2) fusion was identified. The EWSR1-NUDT10 gene fusion is a new fusion type in astroblastoma. The patients were followed up for 76.5, 17.6, 33.7, and 61.3 months, respectively. Three cases experienced tumour recurrences at the spinal cord site, with multiple recurrences in case 4.DiscussionOur study unveiled the distinctive clinicopathological and molecular mutational characteristics of astroblastoma, while also identifying rare mutated genes. Additionally, the detection of MN1 or EWSR1 gene fusion through FISH or next-generation sequencing can provide valuable insights into the molecular mechanisms and aid in the differential diagnosis of astroblastoma.

Tumors with histological features of pilocytic astrocytoma (PA), but with increased mitotic activity and additional high-grade features (particularly microvascular proliferation and palisading necrosis) have often been designated anaplastic pilocytic astrocytomas. The status of these tumors as a separate entity has not yet been conclusively demonstrated and molecular features have only been partially characterized. We performed DNA methylation profiling of 102 histologically defined anaplastic pilocytic astrocytomas. T-distributed stochastic neighbor-embedding (t-SNE) and hierarchical clustering analysis of these 102 cases against 158 reference cases from 12 glioma reference classes revealed that a subset of 83 of these tumors share a common DNA methylation profile that is distinct from the reference classes. These 83 tumors were thus denominated DNA methylation class anaplastic astrocytoma with piloid features (MC AAP). The 19 remaining tumors were distributed amongst the reference classes, with additional testing confirming the molecular diagnosis in most cases. Median age of patients with MC AAP was 41.5 years. The most frequent localization was the posterior fossa (74%). Deletions of CDKN2A/B (66/83, 80%), MAPK pathway gene alterations (49/65, 75%, most frequently affecting NF1, followed by BRAF and FGFR1) and mutations of ATRX or loss of ATRX expression (33/74, 45%) were the most common molecular alterations. All tumors were IDH1/2 wildtype. The MGMT promoter was methylated in 38/83 tumors (45%). Outcome analysis confirmed an unfavorable clinical course in comparison to PA, but better than IDH wildtype glioblastoma. In conclusion, we show that a subset of histologically defined anaplastic pilocytic astrocytomas forms a separate DNA methylation cluster, harbors recurrent alterations in MAPK pathway genes in combination with alterations of CDKN2A/B and ATRX, affects patients who are on average older than those diagnosed with PA and has an intermediate clinical outcome.

Radiomics and genomics represent two of the most promising fields of cancer research, designed to improve the risk stratification and disease management of patients with prostate cancer (PCa). Radiomics involves a conversion of imaging derivate quantitative features using manual or automated algorithms, enhancing existing data through mathematical analysis. This could increase the clinical value in PCa management. To extract features from imaging methods such as magnetic resonance imaging (MRI), the empiric nature of the analysis using machine learning and artificial intelligence could help make the best clinical decisions. Genomics information can be explained or decoded by radiomics. The development of methodologies can create more-efficient predictive models and can better characterize the molecular features of PCa. Additionally, the identification of new imaging biomarkers can overcome the known heterogeneity of PCa, by non-invasive radiological assessment of the whole specific organ. In the future, the validation of recent findings, in large, randomized cohorts of PCa patients, can establish the role of radiogenomics. Briefly, we aimed to review the current literature of highly quantitative and qualitative results from well-designed studies for the diagnoses, treatment, and follow-up of prostate cancer, based on radiomics, genomics and radiogenomics research.