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PubMed2000

Streptococcus pyogenes collected in Torino (northwest Italy) between 1983 and 1998: survey of macrolide resistance and trend of genotype by RAPD.

We surveyed macrolide resistance in 1,086 isolates of Streptococcus pyogenes, collected between 1983 and 1998, from throat swabs of children with untreated pharyngotonsillitis living in Torino (northwest Italy). In 1983 and 1985, the frequency of erythromycin resistance was 10%, and from 1990 to 1992 it was 4%. However, it rose to 16.6% in 1994 and reached 51% in 1996 before decreasing to 38.5% in 1998. Characterization of the phenotype of resistant isolates revealed the prevalence of constitutive resistance (CR) in 1996, whereas the M phenotype, characterized by resistance to 14- and 15-membered macrolides with susceptibility to clindamycin and streptogramin B, prevailed in 1998. Moreover, in 1997 we observed an increase in the frequency of autoagglutinating bacteria and, in 1998, of OF-negative S. pyogenes. Meanwhile, penicillin tolerance, assessed in the isolates collected from 1990 to 1996, decreased and disappeared. Random amplification of polymorphic DNA (RAPD) was used to obtain the genomic profile of 32 S. pyogenes strains. Four main DNA profiles were demonstrated, generally related to the macrolide-resistance phenotype and for the major part to the T serotype. These results indicate that RAPD is reliable as a first screening method in the epidemiological characterization of resistant S. pyogenes.

Anti-Bacterial Agents↗

PubMed2006

Wide genomic analysis of human endometrial receptivity: new times, new opportunities.

Microarray technology has broadened the insight into many research fields allowing scientists to analyse the expression of many genes in quick and efficient experiments aimed at translating these findings into clinical applications. In reproductive medicine, researchers have exploited microarrays to increase understanding of the molecular mechanisms involved in endometrial receptivity and how a possible therapeutic translation can be feasible. In the last 4 years, several studies have focused on the genomics of the human endometrium in different physiological and pathological conditions, and these studies have generated a large amount of information about the regulation and dysregulation of the window of implantation (WOI) genes in fertile, subfertile and refractory conditions. However, the key molecules/mechanisms in endometrial receptivity remain to be elucidated. In this comprehensive review, we have analysed the available results obtained in our own and other laboratories, defining the genomic profile of the receptive endometrium in different situations and its possible clinical application.

Animals↗

PubMed1987

Antigen detection with monoclonal antibodies for the diagnosis of adenovirus gastroenteritis.

A monoclonal antibody-based enzyme immunoassay (EIA) was developed for direct detection of enteric adenoviruses in stool specimens from individuals with gastroenteritis. Tests specific for each of the enteric adenoviruses, adenovirus type 40 (Ad 40) and type 41 (Ad 41), were designed. The sensitivity of the assay was determined by comparing the results of the EIA with isolation of virus in Graham 293 cells from stools that contained particles having adenovirus morphology. The standard for specificity was analysis of adenovirus genome profiles after digestion with SmaI endonuclease. The sensitivity was 95.8% (23 of 24) for Ad 40 and 97.1% (34 of 35) for Ad 41. The specificity was 95.7% (45 of 47) and 97.2% (35 of 36), respectively. The two type-specific monoclonal antibodies could be mixed in an EIA for identification of enteric adenoviruses in stools without loss of reactivity in either type. The EIA permits rapid diagnosis and type-specific identification of enteric adenoviruses in gastroenteritis.

Adenoviridae Infections↗

PubMed1993

Penicillin-resistant Streptococcus pneumoniae strains recovered in Houston: identification and molecular characterization of multiple clones.

A sample of 48 penicillin-resistant Streptococcus pneumoniae (PRSP) strains recovered between January 1989 and May 1991, primarily from infected children in Houston, was characterized by multilocus enzyme electrophoresis and repetitive extragenic palindromic-polymerase chain reaction genomic profiling. A heterogeneous array of 22 clonal genotypes was identified, but 64% of the PRSP strains in the sample were assigned to five clones that are closely similar in overall chromosomal character and express serotype 6 capsule. A close genetic association between these five clones and penicillin-resistant 6B clones recovered in Alaska, Iceland, and Spain was identified by multilocus enzyme electrophoresis. Taken together, the results suggest either that the common resistant 6B clones in Alaska, Iceland, Spain, and Houston have a recent ancestor or that isolates of a certain pneumococcal phylogenetic lineage are more likely to develop penicillin resistance.

Base Sequence↗

PubMed2004

Genome-wide expression profiling reveals genes associated with amphotericin B and fluconazole resistance in experimentally induced antifungal resistant isolates of Candida albicans.

OBJECTIVES: The aim of this study was to identify changes in the gene expression profile of Candida albicans associated with the acquisition of experimentally induced resistance to amphotericin B and fluconazole. METHODS: C. albicans SC5314 was passed in increasing concentrations of amphotericin B to generate isolate SC5314-AR. Susceptibility testing by Etest revealed SC5314-AR to be highly resistant to both amphotericin B and fluconazole. The gene expression profile of SC5314-AR was compared with that of SC5314 using DNA microarray analysis. Sterol composition was determined for both strains. RESULTS: Upon examination of MICs of antifungal compounds, it was found that SC5314-AR was resistant to both amphotericin B and fluconazole. By microarray analysis a total of 134 genes were found to be differentially expressed, that is up-regulated or down-regulated by at least 50%, in SC5314-AR. In addition to the cell stress genes DDR48 and RTA2, the ergosterol biosynthesis genes ERG5, ERG6 and ERG25 were up-regulated. Several histone genes, protein synthesis genes and energy generation genes were down-regulated. Sterol analysis revealed the prevalence of sterol intermediates eburicol and lanosterol in SC5314-AR, whereas ergosterol was the predominant sterol in SC5314. CONCLUSION: Along with changes in expression of these ergosterol biosynthesis genes was the accumulation of sterol intermediates in the resistant strain, which would account for the decreased affinity of amphotericin B for membrane sterols and a decreased requirement for lanosterol demethylase activity in membrane sterol production. Furthermore, other genes are implicated as having a potential role in the polyene and azole antifungal resistant phenotype.

Amphotericin B↗

PubMed2026

Primary mismatch repair deficient glioma, IDH-wildtype and H3-wildtype: A giant cell tumor with potential for long-term survival occurring at all ages.

BACKGROUND: Replication repair deficiency is associated with increased risk of developing malignant gliomas. The aim of this study was to investigate primary mismatch repair deficient gliomas (PMMRDGs), a group of IDH-wildtype and H3-wildtype gliomas that is enriched among patients with CMMRD and Lynch syndrome. METHODS: We investigated how PMMRDGs differ from other gliomas with respect to DNA methylation profile, genomic alterations, histopathology, and clinical outcomes. RESULTS: PMMRDGs occur in pediatric, adolescents and the elderly, falling in two related methylation clusters and are characterized by a high frequency of replication repair deficiency. Histology showed multinucleated giant cells, and immunohistochemistry demonstrated loss of MMR protein expression. Survival analysis revealed long-term survival in patients with high mutational burden (>50 mut/Mb) and an intact chromosome 9p region, which was validated in an independent reference cohort. CONCLUSIONS: Overall, our findings indicate that PMMRDGs represent a distinct type of IDH-wildtype gliomas with potential for long-term survival likely driven by immune activation.

Humans↗

PubMed2006

Chromosomal and microsatellite instability of adenocarcinomas and dysplastic lesions (DALM) in ulcerative colitis.

Longstanding ulcerative colitis (UC) is associated with a high risk of developing UC-related colonic adenocarcinoma (UCC). These carcinomas originate from nonadenomatous dysplastic regions referred to as dysplasia associated lesion or mass (DALM). We evaluated chromosomal and microsatellite instability (MSI) in 21 DALM/UCCs. Chromosomal instability was determined by high-resolution array comparative genomic hybridization with a 3500-element BAC-PAC array. MSI was assessed with markers BAT25 and BAT26 and by immunohistochemical analysis of mismatch repair genes. Comparative genomic hybridization revealed frequent losses of array clones (>20% of tumors) at chromosome arms 4p, 5q, and 18q, frequent gains of array clones (>20% of tumors) were found at 1q, 5p, 6p, 7p, 7q, 8p, 8q, 11p, 11q, 12q, 14q, 17q, 19q, 20p, and 20q. The pattern of alterations is dominated by gains on 5p and 20q with loss of 4p, all of which were already present in a patient with carcinoma in situ. Immunohistochemical analysis of mismatch repair genes MLH1, PMS2, MSH2, and MSH6 showed negative immunostaining in 1 neoplasm (5%). MSI of BAT25 and BAT26 was seen in 3 tumors (14%) including the neoplasm with aberrant immunostaining. In conclusion, we constructed a genomic profile of DALM/UCC including several novel genetic alterations. Further, we found a low percentage of MSI. Thus, DALM/UCCs display profound chromosomal instability, but this is not associated with concurrent MSI.

Adenocarcinoma↗

PubMed1999

Complex genomic and phenotypic characterization of the related species Staphylococcus carnosus and Staphylococcus piscifermentans.

On the basis of numerical analysis of 100 phenotypic features, the strains of two species, Staphylococcus carnosus and Staphylococcus piscifermentans, were differentiated into two separate phenons corresponding with the macrorestriction patterns of their genomic DNA, as well as with the results of ribotyping and PCR amplification of enterobacterial repetitive intergenic consensus sequences. One of the S. carnosus strains, the F-2 strain, was shown to be marginal, exhibiting the lowest genomic and phenotypic similarity to the S. carnosus type strain DSM 20501T. Two of the strains studied (strains S. carnosus SK 06 and S. piscifermentans SK 05) were phenotypically convergent, forming a separate phenon. They were phenotypically similar, even though the genomic DNA of one of them was homologous with that of the S. carnosus type strain, whereas that of the other was homologous with the genomic DNA of the S. piscifermentans type strain. In such cases, fingerprinting methods (particularly macrorestriction analysis and ribotyping) served as important correctives, as they allow phenotypically convergent strains to be distinguished on the basis of their genomic profiles. The results of this paper support the proposal for the new species Staphylococcus condimenti as well as the new subspecies Staphylococcus carnosus subsp. utilis.

Bacterial Typing Techniques↗

PubMed1992

The pathogenicity of two porcine rotaviruses differing in their in vitro growth characteristics and genes 4.

The pathogenicity of two rotavirus variants, 4F and 4S, obtained following adaptation to cell culture of rotavirus from a diarrhoeic pig in China, was compared by serial passage in 24 gnotobiotic piglets. The rotavirus variants have markedly different growth characteristics in vitro, and their genome profiles differ only in the relative migration of genes 4. Both cell culture-grown variants replicated to an equal extent in gnotobiotic piglets and neither caused disease, although weight gain was slightly affected in piglets inoculated with the 4F variant. During five serial pig-to-pig passages, variant 4F became highly pathogenic at the fourth and fifth passages, causing severe diarrhoea and weight loss, and premature death in two animals. Piglets inoculated with rotavirus variant 4S remained healthy during all passages although weight gain was slightly affected. Mean duration and peak infectivity titres of virus shedding were similar for both variants. Thus, variant 4F, which grew slowly and produced small plaques in vitro and had the faster migrating gene 4, was pathogenic in pigs, whereas variant 4S was apathogenic.

Adaptation, Biological↗

PubMed1996

Type characterisation and antibiotic susceptibility of Burkholderia (Pseudomonas) cepacia isolates from patients with cystic fibrosis in the United Kingdom and the Republic of Ireland.

The spread of Burkholderia cepacia among cystic fibrosis (CF) patients in the UK prompted an investigation into whether an epidemic strain was responsible. A total of 366 B. cepacia isolates from 178 CF patients in 17 centres was examined by ribotyping and pulsed-field gel electrophoresis (PFGE). Associations were also sought between antibiotic resistance and strain type. More than 50 ribotype patterns were found but one, termed ribotype 1, was identified from 68 patients in eight centres. One centre had a single patient with this type while, in others, most or all patients harboured this organism. Small clusters of apparent cross-colonisation within centres were also evident for some other ribotypes. PFGE confirmed that ribotype 1 isolates were genetically similar. Ribotype 1 isolates were not markedly more resistant to antimicrobial agents than were other isolates, and the MICs of individual antibiotics were no more tightly clustered for ribotype 1 isolates than for others. Most isolates were resistant to ciprofloxacin, amikacin, gentamicin, tobramycin, carbenicillin, cefuroxime, cefotaxime, imipenem, biapenem, chloramphenicol, tetracycline, trimethoprim and sulphamethoxazole, but > or = 77% were susceptible to ceftazidime, piperacillin, piperacillin/ tazobactam and meropenem. We conclude that numerous strains of B. cepacia colonise CF patients in the UK and Ireland but that one epidemic strain has spread in at least eight centres. Isolates of this strain appear homogenous in total genomic profile but very variable in antibiotic susceptibility.

Bacterial Typing Techniques↗

PubMed2005

Mycoplasma amphoriforme sp. nov., isolated from a patient with chronic bronchopneumonia.

A mycoplasma was isolated from the sputum of an immunodeficient patient with recurrent bronchitis. The isolate designated strain A39T was very fastidious and atypical for a mycoplasma in its colonial appearance. Classical biochemical tests for mycoplasma speciation could not differentiate the isolate from the pathogens Mycoplasma pneumoniae and Mycoplasma genitalium and serological identification as a recognized Mycoplasma species was lacking. Specific PCR detection for these two species was negative. Subsequently, other strains were isolated from human patients that appeared to be similar to strain A39T in their physiological and genetic characteristics. Analysis of the 16S rRNA gene placed strain A39T and other isolates in the pneumoniae group of mycoplasmas, with the highest sequence similarity to Mycoplasma testudinis (96.8 %), but with only 93.0 % similarity to M. pneumoniae and M. genitalium. Examination of the 16S-23S rRNA internally transcribed spacer sequence, protein electrophoresis profile, genome size and serological reactions indicated that this organism represents a novel species, for which the name Mycoplasma amphoriforme sp. nov. is proposed, with strain A39T (=NCTC 11740T=ATCC BAA-992T) as the type strain.

Bronchopneumonia↗

PubMed2003

Molecular comparison of bacterial isolates from blood with strains colonizing pharynx and intestine in immunocompromised patients with sepsis.

Most causative organisms of sepsis in immunocompromised patients are the same species as those that colonize their own nasopharynx or intestinal tract. To determine whether the strains recovered from blood originate mainly from patients' own flora, isolates from blood and throat and/or stool were investigated by genomic analyses. Surveillance cultures of throat and stool were taken prospectively from cancer patients being treated with intensive chemotherapy followed by haematopoietic stem-cell transplantation. In those cases of sepsis in which the isolate from blood was the same species as that from the throat and/or stool, the genomic profiles of the isolates were compared by PFGE. Ten cases of blood culture-positive sepsis were documented in six of 14 subjects during a 2 year period; isolates of Pseudomonas aeruginosa, Staphylococcus epidermidis, Enterococcus sp., viridans streptococci and Fusobacterium sp. were recovered from blood. In five of seven cases in which the blood isolate was the same species as that from the throat or stool, the genotypes of the isolates from both sites were identical. In the majority of immunocompromised patients, the causative organisms of bloodstream infections originated mainly from their own flora.

Adolescent↗

PubMed2025

scMultiNODE: Integrative and Scalable Framework for Multi-Modal Temporal Single-Cell Data.

Measuring single-cell genomic profiles at different timepoints enables our understanding of cell development. This understanding is more comprehensive when we perform an integrative analysis of multiple measurements (or modalities) across various developmental stages. However, obtaining such measurements from the same set of single cells is resource-intensive, restricting our ability to study them jointly. We introduce scMultiNODE, an unsupervised integration model that combines gene expression and chromatin accessibility measurements in developing single cells, while preserving cell type variations and cellular dynamics. First, scMultiNODE uses a scalable, Quantized Gromov-Wasserstein optimal transport to align a large number of cells across different measurements. Next, it utilizes neural ordinary differential equations to explicitly model cell development with a regularization term to learn a dynamic latent space. Experiments on six real-world developmental single-cell datasets demonstrate that scMultiNODE can integrate temporally profiled multi-modal single-cell measurements more effectively than existing methods that focus on cell type variations and often overlook cellular dynamics. We also demonstrate that scMultiNODE's joint latent space facilitates several insightful downstream analyses of single-cell development, including the investigation of complex cell trajectories and the enabling of cross-modal label transfer. The data and code are publicly available at https://github.com/rsinghlab/scMultiNODE.

autoencoders↗

PubMed2004

Control of yeast filamentous-form growth by modules in an integrated molecular network.

On solid growth media with limiting nitrogen source, diploid budding-yeast cells differentiate from the yeast form to a filamentous, adhesive, and invasive form. Genomic profiles of mRNA levels in Saccharomyces cerevisiae yeast-form and filamentous-form cells were compared. Disparate data types, including genes implicated by expression change, filamentation genes known previously through a phenotype, protein-protein interaction data, and protein-metabolite interaction data were integrated as the nodes and edges of a filamentation-network graph. Application of a network-clustering method revealed 47 clusters in the data. The correspondence of the clusters to modules is supported by significant coordinated expression change among cluster co-member genes, and the quantitative identification of collective functions controlling cell properties. The modular abstraction of the filamentation network enables the association of filamentous-form cell properties with the activation or repression of specific biological processes, and suggests hypotheses. A module-derived hypothesis was tested. It was found that the 26S proteasome regulates filamentous-form growth.

Cell Cycle↗

PubMed2005

Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression.

Immunoaffinity purification of polyribosomes (polysomes) from crude leaf extracts of Arabidopsis (Arabidopsis thaliana) was achieved with transgenic genotypes that overexpress a translational fusion of a ribosomal protein (RP) with a His(6)-FLAG dual epitope tag. In plants with a cauliflower mosaic virus 35S:HF-RPL18 transgene immunopurification with anti-FLAG agarose beads yielded 60-Svedberg ribosomal subunits, intact 80-Svedberg monosomes and polysomes. Sucrose density gradient fractionation of the purified complexes demonstrated that the distribution of polysome size was similar in crude cell extracts and the purified complexes. The immunopurified complexes included putative cytosolic RPs of Arabidopsis and ribosome-associated proteins, as well as full-length transcripts of high and low abundance. Whole-genome profiling using long DNA oligonucleotide-based microarrays provided a high level of reproducibility between polysomal mRNA samples immunopurified from two independent biological replicates (r approximately 0.90). Comparison of immunopurified and total cellular RNA samples revealed that for most of the genes, the mRNAs were associated with the epitope-tagged polysomal complexes, with an average relative level of association of 62.06% +/- 4.39%. The results demonstrate that the immunopurification of polysomes can be a valuable tool for the quantification of mRNAs present in translation complexes in plant cells. This technology can be extended to evaluation of mRNA populations at the cell- or tissue-specific level by regulation of the tagged RP with distinct promoters.

Arabidopsis↗

PubMed2026

The future of precision oncology and artificial intelligence in Belgium: scenarios and policy responses.

PURPOSE: Precision medicine, also known as personalized medicine, enables the provision of tailored health services to patients. In the prevention, early detection, and treatment of cancers, precision medicine is highly promising, given the increasing use of genomic profiling for diagnosis and adapting therapies in several tumor types. Artificial Intelligence (AI) can support this process by analyzing vast amounts of relevant data. However, high-quality data and financial investments in the health system are essential for the implementation of precision medicine and AI solutions in routine cancer care. DESIGN/METHODOLOGY/APPROACH: Building on the quantitative outcomes of a foresight exercise published in another study, this article collects qualitative data to gain more detailed insights into the future of precision oncology in Belgium and discusses the role of AI in this field. It reports the results of a series of expert workshops, focusing on four hypothetical future scenarios that are centered around technological and economic issues that must be overcome for the widespread use of precision oncology in Belgium. FINDINGS: The study concludes that all four scenarios discussed in the workshops would require supportive policy measures in Belgium, which should go beyond mere technological and economic considerations, such as involving patient associations and the public in policy design or creating multi-disciplinary expert groups for precision medicine. ORIGINALITY/VALUE: To the best of our knowledge, this is the first study to employ foresight methodology to illustrate possible future scenarios, scrutinize feasible approaches for implementing precision oncology in Belgium, and discuss the use of AI in this context.

Belgium↗

PubMed2025

Liquid Biopsy in Hematologic Malignancies: Advances, Challenges, and Future Directions.

Hematologic malignancies are cancers that affect the bone marrow, lymphatic system, and hematopoietic cells, resulting in various cancer subtypes and clinical manifestations. Currently, tissue biopsy in hematological malignancies is typically performed for genomic profiling and has limitations such as invasiveness, lengthy procedures, and high expense. On the other hand, liquid biopsy serves as an emerging tool used for examining the blood or other bodily fluids of patients, for the purpose of identifying genetic mutations, biomarkers, or cancer-related substances. Liquid biopsy biomarkers include circulating tumor DNA (ctDNA), microRNA (miRNA), and exosomes. In the context of hematological malignancies, these biomarkers offer valuable insights into disease etiology, enabling effective disease monitoring and guiding treatment decisions owing to their differential expression patterns. This review critically examines the recent advancements and effectiveness of liquid biopsy biomarkers in the areas of diagnosis, therapy, and monitoring. The challenges and future directions of liquid biopsy for hematological malignancies are also discussed.

Humans↗

PubMed2026

Tumor Mutational Concordance and Recurrence Timing in Hepatocellular Carcinoma.

INTRODUCTION: In hepatocellular carcinoma (HCC), intrahepatic recurrence includes true recurrence from clonal relapse and multicentric recurrence from de novo tumorigenesis. Recurrence timing is used to distinguish these types; however, its accuracy remains unclear. This study aimed to classify recurrent tumors based on somatic mutational concordance and assess the validity of recurrence timing. METHODS: Whole-exome sequencing was performed on paired primary and recurrent HCC tumors from 49 patients enrolled in a prospective institutional omics project. Tumors with ≥ 10 shared somatic mutations were classified as true recurrence. Clinicopathological features, recurrence timing, driver mutation patterns, and survival outcomes were compared between recurrence types. Mutational concordance was quantified using shared variant counts and the Jaccard similarity index. RESULTS: Of the 49 patients, 22 (44.9%) showed true recurrence and 27 (55.1%) had multicentric recurrence. Multicentric recurrence tumors harbored no shared variants or only a single shared variant with the primary tumor. True recurrence was associated with significantly higher concordance in histological differentiation and Edmondson-Steiner grading and greater retention of CTNNB1, TP53, ARID1A, and KEAP1 mutations. The number of shared variants (median: 115 vs. 0, and p < 0.001) and the Jaccard index (median: 0.44 vs. 0.00 and p < 0.001) were significantly higher in the true recurrence group. Recurrence timing was inconsistently correlated with mutational concordance, although a 3-year cutoff yielded significant separation. CONCLUSION: Recurrence timing alone insufficiently reflects clonal relationships. Genomic profiling offers a reliable framework for distinguishing between recurrence types and guiding HCC management.

clonal relapse↗