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PubMed2025

Coxsackievirus A24 variant whole genome sequencing from clinical samples using a three overlapping amplicons strategy.

In January 2024, the Kenya Ministry of Health issued an outbreak alert following a surge in acute hemorrhagic conjunctivitis (AHC) cases along the Kenyan coast. Our investigations identified coxsackievirus A24 variant (CV-A24v) as the causative agent. In this study, we developed a novel whole genome sequencing assay for CV-A24v, and used it to recover three near complete genomes from the 2024 AHC outbreak in Kenya. This method will support future studies on CV-A24v genomic epidemiology and evolution across Kenya and beyond.

Acute Hemorrhagic Conjunctivitis Kenya↗
PubMed2026

Oxford Nanopore Sequencing of Clinical DNA for Identification and Comparative Genomic Analysis of Erysipelothrix piscisicarius.

The genus Erysipelothrix comprises facultative anaerobic, nonspore-forming, gram-positive bacteria that can cause skin infections and severe diseases such as septicemia and endocarditis in humans. Although E. rhusiopathiae is the primary pathogen, other species may also be involved, necessitating accurate identification. However, 16S rDNA sequencing lacks sufficient resolution to differentiate among Erysipelothrix species. In this study, we used Oxford Nanopore Technology (ONT) to directly sequence low-quality DNA extracted from heart valve tissue of a 66-year-old female patient with a fatal case of septicemia and aortic endocarditis. In contrast to 16S rDNA Illumina sequencing and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), which incorrectly identified the pathogen as E. rhusiopathiae, direct sequencing via ONT precisely identified E. piscisicarius as the cause of infection. About 1.47 Mb genome was retrieved from nanopore direct sequencing. Within the E. piscisicarius genome, we detected genes associated with virulence. Phylogenetic analysis showed that our strain clustered with a human-derived E. piscisicarius strain from China and swine-derived strains from Brazil. In conclusion, this study demonstrated that ONT can be used to sequence low-quality DNA extracted directly from patient specimens, obtain a draft bacterial genome, and reliably distinguish between pathogenic species.

Aged↗
PubMedDate not supplied

Design and implementation of magnetization transfer pulse sequences for clinical use.

The transfer of magnetization between a free and a bound pool of spins is described in terms of the respective longitudinal relaxation times and the life times of spins in each pool. The effect of an off resonance radiofrequency (RF) pulse in producing saturation in the bound pool and a consequent decrease in both the available longitudinal magnetization and the T1 of spins in the free pool is described. The effects of increasing duration of the saturating RF pulse on image pixel signal intensity were used to determine values for the decrease in both T1 and the available magnetization in gray and white matter of the brain as well as in muscle, fat, and CSF. At 0.15 T the available magnetization of muscle was reduced by approximately 60% and its T1 was decreased from 350 to 150 ms. The available magnetization of white and gray matter was reduced by 40% and their values of T1 were reduced by 80-110 ms. The reduction in available magnetization was used to increase contrast on proton density weighted or T2-weighted SE pulse sequences. These changes were also used to design inversion recovery (IR) pulse sequences with particular contrast properties. A short inversion time (TI) magnetization transfer (MT) IR (MT-STIR) pulse sequence was used to reduce the signal from normal muscle to zero to produce an angiographic effect in the leg. Increased tissue contrast was observed with a T2-weighted (MT-SE) sequence in a patient with bilateral cerebral infarction and with an MT-IR pulse sequence in a patient who had an intracranial hematoma. Three patients with cerebral tumors showed high lesion contrast with MT-STIR sequences. Components within two tumors were changed to different degrees by MT and in one case change in the brain attributable to recent radiotherapy treatment was only identified with an MT-STIR sequence. Magnetization transfer can be used to manipulate both the available longitudinal magnetization and the T1 of normal and abnormal tissues. The changes in tissue contrast produced by this can be very substantial and are likely to be of importance in clinical imaging.

Adult↗
PubMed2003

Clinical-electroencephalogram patterns at seizure onset in patients with hippocampal sclerosis.

OBJECTIVE: The purpose of this study is to identify specific clinical-electroencephalogram (EEG) patterns at seizure onset in patients with hippocampal sclerosis (HS). METHODS: Sixty-six ictal video-EEG recordings corresponding to 26 patients with HS have been reviewed, focusing on the EEG features found during the first 30 ictal s. The EEG activity has been classified into the following groups: (A) according to spatial distribution: type 1: temporal electrodes on one side; type 2: temporal and adjacent frontal electrodes on one side; and type 3: non-lateralizing electrographic activity; and (B) according to morphology; subtype (a): regular 5-9 Hz rhythmic activity (RA); subtype (b): low-voltage rapid activity, followed by a 5-9 Hz RA; and subtype (c): irregular EEG sharp waves. We analyzed the clinical symptoms sequence and established the relationship with the ictal EEG patterns. RESULTS: Considering spatial distribution and morphology, the most frequent ictal EEG patterns were type 1 (57%), type 2 (37%), and subtype (a): 62%; subtype (b): 27%; and subtype (c): 11%. The sequence of clinical symptoms observed was: aura-->behavioral arrest-->oro-alimentary automatisms-->unilateral hand automatisms. All seizures with aura and including two or more symptoms of the clinical sequence (65%) were associated with a 1a, 1b, 2a or 2b EEG pattern. CONCLUSIONS: The identification of a specific clinical-EEG pattern provides a useful tool for the epileptogenic zone localization in non-invasive pre-surgical assessment of patients with hippocampal sclerosis. SIGNIFICANCE: The identification of a specific clinical-EEG pattern associated to neuroimaging findings and neuropsychological testing allows indicating surgery for the treatment of epilepsy in patients with hippocampal sclerosis, without performing any further complementary studies.

Adult↗
PubMed1998

Branched DNA signal amplification for direct quantitation of nucleic acid sequences in clinical specimens.

In this chapter I have reviewed the development of bDNA as a method for quantitation of nucleic acid targets and the application of this technology to the study of infectious diseases and cell biology. The ability to quantify viral nucleic acids in clinical specimens has led to a better understanding of the pathogenesis of chronic viral infections such as HIV-1, HCV, and HBV. The information provided by these methods can also be important in the management of patients with these infections. The prognostic value of a single baseline HIV-1 RNA level rivals that surgical staging procedures for cancer, which are among the most powerfully predictive tests in medicine (Mellors et al., 1996). These methods have been used to assess rapidly the effects of antiviral therapy, which has both expedited the development of antiviral drugs and improved the management of patients with HIV-1 and HCV infections. bDNA has several characteristics that distinguish it from the quantitative target amplification systems, including better tolerance of target sequence variability, more direct measurement of target, simpler sample preparation, and less sample-to-sample variation. However, the first- and second-generation bDNA assays lacked sensitivity compared with the target amplifications systems. The changes incorporated into the third-generation assays have effectively increased the signal-to-noise ratio to such a high level that the analytical sensitivity of system 8 bDNA approaches that of PCR. In theory, bDNA can be made even more sensitive by increasing both the sample volume and the signal-to-noise ratio. Nonspecific hybridization can be further reduced by finding more effective blockers for the solid phase or by redesigning the amplifier molecule or the solid phase itself. The increased sensitivity may create new applications for the technology in filter and in situ hybridization assays.

Animals↗
PubMed1998

Recombinant Aspergillus fumigatus allergens: from the nucleotide sequences to clinical applications.

Members of the genus Aspergillus are opportunistic pathogens for cold- and warm-blooded animals. They are associated with an impressive spectrum of diseases in humans, ranging from benign colonization of the lung to life-threatening diseases such as invasive aspergillosis or allergic bronchopulmonary aspergillosis (ABPA). Aspergillus fumigatus is the etiological agent identified in most of the Aspergillus-related human diseases and is therefore of particular clinical relevance. A major problem in the diagnosis of A. fumigatus-related complications arises from the lack of standardized fungal extracts. The allergenicity of commercial A. fumigatus extracts depends on many factors including the strain used, growth conditions, harvesting and extraction procedures hampering the development of diagnostic reagents suitable for the discrimination between A. fumigatus-related diseases. Molecular DNA/RNA technologies and biotechnological procedures allow cloning, characterization and production of large amounts of single, highly pure allergens. The development of phage surface display technologies for cloning cDNAs has speeded up the isolation of candidate cDNAs encoding allergens. Screening of an A. fumigatus cDNA library displayed on the surface of phage M13 allowed characterization and production of a panel of allergens identified as proteins with known biological function or as allergens without sequence homology to known proteins. They belong to two functional categories: secreted and cytoplasmic proteins. Secreted allergens are recognized by serum IgE of A. fumigatus-sensitized individuals with or without ABPA, whereas nonsecreted allergens are exclusively recognized by serum IgE of ABPA patients. The dissection of IgE-mediated immune responses to single A. fumigatus allergens allows a discrimination between ABPA and A. fumigatus sensitization with high specificity and sensitivity demonstrating the power of recombinant allergens for the differential diagnosis of A. fumigatus-related pulmonary complications.

Adolescent↗
PubMed1988

Evaluation of methods for detecting human papillomavirus deoxyribonucleotide sequences in clinical specimens.

Specimens from 26 condylomatous lesions, 24 invasive cancer cells, and 33 cervices, without evidence of the diseases, were tested for the presence of human papillomavirus (HPV) types 6, 11, 16, and 18 by Southern blot hybridization, in situ filter hybridization, or in situ tissue hybridization methods. A total of 89% (23 of 26) of the condylomatous lesions contained HPV DNAs, as determined by one or more of the methods. The positive rates for the detection of HPV DNA in condylomas by the different methods were 82% for Southern blot hybridization, 62% for in situ filter hybridization, and 72% for in situ tissue hybridization. Among the specimens from patients with cancer, HPV DNA was found in 83% (19 of 23) by one or more of the methods. Positive rates of 89 and 70%, respectively, were obtained for cancer lesions tested by the filter in situ and Southern blot hybridization methods; however, only 30% of those lesions were positive by the in situ tissue hybridization method. Thirteen percent of the control cervices were positive for HPV DNA by one or more of the assays. With respect to all disease categories, the methods had comparable sensitivities and specificities, except for the in situ tissue hybridization method, which revealed a specificity of 72% for condylomatous lesions and 30% for invasive cancer cells.

Cervix Uteri↗
PubMedDate not supplied

[Sequence of clinical changes and evolution of MR images in a case of chronic SSPE].

Slow course case of subacute sclerosing panencephalitis is reported. The onset was at the age of 16 years and death followed after 5 years. He was observed during nine successive hospitalizations and the authors describe the changing clinical symptomatology parallelly with successive EEG records and brain MR imaging evolution. Successive phases of the disease were associated with hyperintense changes in T2-weighted.images, and were situated initially in occipital lobes, and involved later on periventricular areas and finally the whole white matter of both cerebral hemispheres. Subcortical brain atrophy developed parallelly.

Adolescent↗
PubMed1990

Quantitative evaluation of hyaline cartilage disorders using flash sequence. II. Clinical applications.

In a prospective clinical study 24 normal volunteers and 106 patients with acute and chronic arthritis, osteoarthritis and post-traumatic alterations of the knee joints were examined. Using the parameters A and M 98 per cent of the pathologic cartilages and 74 per cent of the normal cartilages could be identified. In addition 78.5 per cent were correctly categorized in 5 cartilage classes. The A/M classification proved to be a fast and specific method for evaluation of cartilage disorders with special promise for follow-up examinations during therapy.

Adolescent↗
PubMedDate not supplied

[Sonic and ultrasonic instruments for endodontics. 2. Operative sequence and clinical advantages].

The authors describe the differential characteristics between sonic and ultrasonic endodontic devices: the former type is pneumatic and uses the air coning from the odontoiatric chair that gives to the endodontic instrument only a lateral way of swinging. The latter type changes the ultrasonic activity coming from piezoeletric phenomena into swinging mechanical energy (operating at 25 KHz). The authors specify the characteristics of endodontic instruments and explain their operating ways, demonstrating that reaming by endosonic instruments increases effects of hypochlorite. They also describe the operating train, pausing on the opportunity that the root canal should be manually probed, measured and reamed up to a diameter that gives sufficient space to the file vibration. They conclude listing the advantages that gives the correct use of sonic and ultrasonic devices; they also augur that with their use endodontics could have a greater diffusion.

Dental Pulp Diseases↗
PubMed2003

Bacteria detected by culture and 16S rRNA sequencing in maxillary sinus samples from intensive care unit patients.

OBJECTIVES/HYPOTHESIS: In critically ill patients, the occurrence of artificial ventilation-acquired sinus disease is common. A possible sinus bacterial infection is occult and is combined with diagnostic difficulties. Culture as a method has limited capacity to verify the presence of bacteria and leaves unanswered the question of a possible infective agent because bacteria are difficult to grow when killed or suppressed by current antibiotic therapy. Hitherto unidentified micro-organisms are also possible in the microenvironments of maxillary sinuses. STUDY DESIGN: Prospective case series. METHODS: Twenty maxillary sinus samples (17 aspirates and 3 lavages) from nine critically ill patients with possible infectious disease were investigated by broad-range 16S rRNA polymerase chain reaction followed by sequencing. These results were compared with the previous culture results from gingiva (passage route), maxillary sinus absorption, and mucosa samples. RESULTS: The contaminations were rare (2 of 20) and corresponded well to culture results. One previously undiagnosed bacterium was found. Two aspirates were negative on both culture and polymerase chain reaction, whereas the corresponding maxillary sinus mucosal cultures had been positive. CONCLUSIONS: Applying a low-contamination maxillary sinuses sampling technique makes 16S rRNA sequencing clinically useful. The polymerase chain reaction and culture results were generally comparable. However, by polymerase chain reaction, bacteria were found that were missed by culturing. Some aspirates were free of bacterial remnants on 16S rRNA polymerase chain reaction, but corresponding mucosal cultures were positive. This could indicate that infection is induced within the tissue. It also indicates that infectious agents introduced into the sinuses may have routes other than the ostium. Further clinical use of 16S rRNA sequencing is required to enlarge our knowledge in applied microbiology and paranasal sinus disease.

Bacteria↗
PubMed2026

Genomic Sequencing in Neonatal Encephalopathy and Suspected Hypoxic-Ischaemic Encephalopathy: A Systematic Review.

BACKGROUND: Neonatal encephalopathy (NE) is a major cause of neonatal mortality and long-term neurological disability. Although hypoxic-ischaemic encephalopathy (HIE) is the most common cause, several genetic disorders may mimic or coexist with hypoxic-ischaemic injury. Next-generation sequencing has emerged as a promising diagnostic tool in this setting. This systematic review evaluated the current evidence on genomic sequencing in NE. MATERIAL AND METHODS: A systematic review was conducted according to PRISMA 2020 guidelines and prospectively registered in PROSPERO. PubMed/MEDLINE, Embase, and Scopus were searched from inception to June 2026. Eligible studies included neonates (≤28 days) with NE, suspected or confirmed HIE, HIE mimics, or unexplained NE who underwent genomic sequencing. Whole-exome sequencing (WES), whole-genome sequencing (WGS), clinical exome sequencing (CES), rapid genomic sequencing, and targeted next-generation sequencing panels were considered. Study quality was assessed using the Newcastle-Ottawa Scale. RESULTS: Seven studies met the inclusion criteria. Considerable heterogeneity was observed regarding patient selection, sequencing strategies, and reported outcomes. Among diagnostic sequencing studies, diagnostic yield ranged from 23.5% to 53.1%. Pathogenic and likely pathogenic variants were identified in genes associated with developmental and epileptic encephalopathies, metabolic disorders, mitochondrial diseases, and neurodevelopmental syndromes, including SCN2A, KCNQ2, CACNA1A, STXBP1, PTPN11, BCOR, MMUT, COQ2, and GBE1. Genomic sequencing frequently refined or changed the initial diagnosis, improved prognostic assessment and genetic counselling, and, in selected cases, guided disease-specific treatment. One study investigated genetic susceptibility to hypoxic-ischaemic injury rather than diagnostic sequencing. CONCLUSIONS: Genomic sequencing provides clinically meaningful diagnoses in a substantial proportion of neonates with unexplained NE or atypical HIE presentations. Current evidence supports integrating genomic sequencing into the diagnostic evaluation of selected infants, although larger prospective studies are needed to define its optimal timing, clinical utility, and cost-effectiveness.

Humans↗
PubMed2002

Evaluation of outpatient hysteroscopy and ultrasonography in the diagnosis of endometrial disease.

OBJECTIVE: To develop a multivariable approach to determine the added value of tests in routine practice where some diagnostic information is already available from clinical history. METHODS: Multivariable logistic regression models were built in a stepwise fashion, considering the clinical sequence used in the rapid access ambulatory diagnosis clinic (clinical history followed by transvaginal ultrasonography and hysteroscopy). The reference standard for confirmation of diagnosis was endometrial biopsy. The diagnostic accuracy of the models was determined by the area under the receiver operating characteristic curve. RESULTS: The area under the receiver operating characteristic curve for the model including historical features alone was 0.78. When hysteroscopy and ultrasonography were each added to the model, it increased to 0.81 (P =.008 for improvement) and 0.82 (P =.02 for improvement), respectively. CONCLUSION: The type of stepwise analysis we have developed is crucial in facilitating meaningful clinical interpretation about the value of diagnostic technology. Our finding that hysteroscopy or ultrasonography marginally but significantly increased the prediction of serious endometrial pathology above that predicted from patient history alone needs validation in an independent data set. The use of this approach is recommended when evaluating strategies for diagnosis.

Adult↗
PubMed2001

Analysis on distribution of insertion sequence IS431 in clinical isolates of staphylococci.

Distribution of insertion sequence IS431 in clinical isolates of Staphylococcus aureus, Staphylococcus epidermidis, and Staphylococcus haemolyticus was investigated. Except for methicillin susceptible-S. aureus (MSSA), IS431 was detected in all isolates of the three staphylococcal species. In MSSA, only 20% of isolates with distinct coagulase types and genetic types possessed IS431. In a few MSSA isolates, an IS431 variant with internal deletion was found.

Base Sequence↗
PubMed2005

Clinical bioinformatics.

Clinical bioinformatics provides biological and medical information to allow for individualized healthcare. In this review, we describe the uses of clinical bioinformatics. After the analysis of the complete human genome sequences, clinical bioinformatics enables researchers to search online biological databases and use the biological information in their medical practices. The data obtained from using microarray is extremely complicated. In clinical bioinformatics, selecting appropriate software to analyze the microarray data for medical decision making is crucial. Proteomics strategy tools usually focus on similarity searches, structure prediction, and protein modeling. In clinical bioinformatics, the proteomic data only have meaning if they are integrated with clinical data. In pharmacogenomics, clinical bioinformatics includes elaborate studies of bioinformatics tools and various facets of proteomics related to drug target identification and clinical validation. Using clinical bioinformatics, researchers apply computational and high-throughput experimental techniques to cancer research and systems biology. Meanwhile, researchers of bioinformatics and medical information have incorporated clinical bioinformatics to improve health care, using biological and medical information. Using the high volume of biological information from clinical bioinformatics will contribute to changes in practice standards in the healthcare system. We believe that clinical bioinformatics provides benefits of improving healthcare, disease prevention and health maintenance as we move toward the era of personalized medicine.

Computational Biology↗
PubMed2004

Clinical relevance of optineurin sequence alterations in Japanese glaucoma patients.

PURPOSE: To study the clinical relevance of sequence alterations in the optineurin gene (OPTN) among Japanese patients with open-angle glaucoma, including both primary open-angle glaucoma (POAG) and normal tension glaucoma (NTG). METHODS: Genomic DNA was isolated from 83 patients with open-angle glaucoma (55 with POAG and 28 with NTG) and 58 control subjects. The 13 exons of OPTN corresponding to the coding region were amplified by polymerase chain reaction and directly sequenced. Clinical factors were compared between glaucoma patients with and without a certain nucleotide change. RESULTS: The reported heterozygous mutations, c.458G > A(Glu50Lys) in exon 4 and c.691_692insAG in exon 6, were not found in any glaucoma patients or control subjects. The reported c.603T > A(Met98Lys) in exon 5 was significantly more prevalent in the POAG (8/55, 14.5%, p=0.0147) and NTG (4/28, 14.2%, p=0.0369) patients, and even in both the POAG and NTG patients combined (12/83, 14.4%, p=0.0149, Fisher exact probability test), than in the control subjects (1/58, 1.7%). The rates of the reported c.1944G > A(Arg545Gln) in exon 16 were not significantly different between open-angle glaucoma patients (3/83, 3.6%) and control subjects (4/58, 6.8%). In addition, a heterozygous change, c.412G > A(Thr34Thr) in exon 4 was found in 18 (21.6%) open-angle glaucoma patients and seven (12.0%) control subjects. Another heterozygous change, c.457C > T(Thr49Thr), in exon 4 was found only in three POAG patients. The 18 open-angle glaucoma patients with c.412G > A showed significantly larger cup-to-disc ratios (p=0.0178, Mann-Whitney U test), significantly more deteriorated mean deviations of the visual field in the left eye at the final visit (p=0.0076), and a significantly higher rate of surgery and/or laser history (p=0.0321, Fisher exact probability test) than the 65 open-angle glaucoma patients without the nucleotide change. CONCLUSIONS: Met98Lys is a risk-associated alteration for open-angle glaucoma, including POAG and NTG, in the Japanese population as initially reported. The amino acid-preserving polymorphism, c.412G > A, may be a genetic risk factor for the progression of open- angle glaucoma in this Japanese population.

Adult↗