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Expert Review of Molecular Diagnostics 2023Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly... (Review)
Review
BACKGROUND
Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized and pathogenic organisms from different clinical specimens.
AREAS COVERED
We reviewed the literature evaluating the current state of molecular diagnostics for invasive fungal infections, focusing on current and novel molecular tests such as polymerase chain reaction (PCR), digital PCR, high-resolution melt (HRM), and metagenomics/next generation sequencing (mNGS).
EXPERT OPINION
PCR is highly sensitive and specific, although performance can be impacted by prior/concurrent antifungal use. PCR assays can identify mutations associated with antifungal resistance, non-Aspergillus mold infections, and infections from endemic fungi. HRM is a rapid and highly sensitive diagnostic modality that can identify a wide range of fungal pathogens, including down to the species level, but multiplex assays are limited and HRM is currently unavailable in most healthcare settings, although universal HRM is working to overcome this limitation. mNGS offers a promising approach for rapid and hypothesis-free diagnosis of a wide range of fungal pathogens, although some drawbacks include limited access, variable performance across platforms, the expertise and costs associated with this method, and long turnaround times in real-world settings.
Topics: Humans; Antifungal Agents; Mycoses; Pathology, Molecular; Fungi; Invasive Fungal Infections; Sensitivity and Specificity
PubMed: 37801397
DOI: 10.1080/14737159.2023.2267977 -
Pathologie (Heidelberg, Germany) Jul 2024In recent decades, nephropathology has developed worldwide as a subspeciality of pathology, which requires special methodological and technical equipment to process the... (Review)
Review
In recent decades, nephropathology has developed worldwide as a subspeciality of pathology, which requires special methodological and technical equipment to process the material and specific clinical and pathological expertise to interpret the findings. These special requirements mean that nephropathology is not available at all pathology institutes, but is carried out on a large scale in a few highly specialised centres. The history of nephropathology, or in a narrower sense the specialised histopathological examination of kidney biopsies, began in 1958 with the first use or performance of a kidney biopsy [1]. It thus replaced the practice of urinalysis, which had been common since the Middle Ages, as a diagnostic tool for kidney diseases. Specialised techniques such as immunofluorescence or immunohistology but also electron microscopy are required to assess specific renal changes, for which the examination of renal biopsies is one of the few remaining routine applications today. In Germany and German-speaking countries, the discipline developed thanks to the work of outstanding people in the field of pathology who were primarily involved in this discipline and had the necessary technical and human resources in their laboratories to ensure that these biopsies could be analysed.
Topics: Humans; Kidney Diseases; Biopsy; Kidney; Pathology; Nephrology; Germany
PubMed: 38512473
DOI: 10.1007/s00292-024-01310-z -
Pediatric Radiology Oct 2023The use of magnetic resonance imaging (MRI) in the evaluation of the central extracranial nervous system, namely the brachial and lumbosacral plexuses, is well... (Review)
Review
The use of magnetic resonance imaging (MRI) in the evaluation of the central extracranial nervous system, namely the brachial and lumbosacral plexuses, is well established and has been performed for many years. Only recently after numerous advances in MRI, has image quality been sufficient to properly visualize small structures, such as nerves in the extremities. Despite the advances, peripheral MR Neurography remains a complex and difficult examination to perform, especially in the pediatric patient population, in which the risk for motion artifact and compliance is always of concern. Thus, technical aspects of the MR imaging protocol must be flexible but robust, to balance image quality with scan time, in a patient population of varying sizes. An additional important step for reliably performing a successful MR Neurography examination is the non-technical pre-imaging preparation, which includes patient/family education and open communication with referring teams. This paper will discuss in detail the individual technical and non-technical/operational aspects of peripheral MR Neurography, to help guide in building a successful program in the pediatric population.
PubMed: 37710037
DOI: 10.1007/s00247-023-05759-7 -
The Laryngoscope Jun 2024Structured histopathology (SHP) is a method of analyzing sinonasal tissue to characterize endotypes of chronic rhinosinusitis with nasal polyps (CRSwNP). Allergic fungal... (Comparative Study)
Comparative Study
OBJECTIVE
Structured histopathology (SHP) is a method of analyzing sinonasal tissue to characterize endotypes of chronic rhinosinusitis with nasal polyps (CRSwNP). Allergic fungal rhinosinusitis (AFRS) shares several features with certain endotypes of CRSwNP. Our objective was to compare the histopathology of AFRS and eosinophilic CRSwNP to further understand whether they are separate endotypes or disease entities altogether.
METHODS
A retrospective review of AFRS and CRSwNP patients undergoing endoscopic sinus surgery was performed. Data were collected on demographics, comorbidities, subjective and objective severity scores, and 13-variable SHP reports. CRSwNP patients with >10 eosinophils per high-power field (eCRSwNP) were included. Chi-squared and t-tests were used for statistical analysis.
RESULTS
A total of 29 AFRS and 108 eCRSwNP patients were identified. AFRS patients were younger and more often Black. Symptom severity scores (SNOT-22, Lund-MacKay, and Lund-Kennedy) were uniform between groups. AFRS patients had a higher rate of Charcot-Leyden crystals (41.4% vs. 10.2%; p < 0.001). Severe degree of inflammation, eosinophilic inflammatory predominance, eosinophil aggregates, subepithelial edema, and basement membrane thickening were common in both groups, and their rates were not statistically significantly different between groups. Metaplasia, ulceration, fibrosis, and hyperplastic/papillary change rates were low (<30%) and similar between groups.
CONCLUSION
The SHP of eCRSwNP and AFRS are highly consistent, which suggests AFRS is a severe subtype of CRSwNP overall rather than a separate disease entity. This also lends credence to AFRS belonging on the endotypic spectrum of CRSwNP.
LEVEL OF EVIDENCE
3 Laryngoscope, 134:2617-2621, 2024.
Topics: Humans; Sinusitis; Nasal Polyps; Male; Female; Retrospective Studies; Chronic Disease; Middle Aged; Adult; Rhinitis; Rhinitis, Allergic; Mycoses; Eosinophils; Endoscopy; Allergic Fungal Sinusitis; Rhinosinusitis
PubMed: 38073117
DOI: 10.1002/lary.31225 -
The American Surgeon Dec 2023Completion pancreatectomy (C.P.) is one acceptable treatment of choice in clinical scenarios such as management of post-pancreatectomy complications and recurrence in... (Review)
Review
BACKGROUND/OBJECTIVE (S)
Completion pancreatectomy (C.P.) is one acceptable treatment of choice in clinical scenarios such as management of post-pancreatectomy complications and recurrence in the pancreatic remnant. Studies referring to completion pancreatectomy as a distinct operation are limited, without emphasizing at the operation itself, rather reporting completion pancreatectomy as a possible option for treatment of various diseases. The identification of indications of CP in various pathologies and the clinical outcomes are therefore mandatory.
METHODS
A systematic literature search was performed in the Pubmed and Scopus Databases (February 2020),guided by the PRISMA protocol, for all studies reporting CP as a surgical procedure with reference at indications for performing it combined with postoperative morbidity and/or mortality.
RESULTS
Out of 1647 studies, 32 studies from 10 countries with 2775 patients in total, of whom 561 (20.2%) CPs met the inclusion criteria and were included in the analysis. Inclusion year ranged from 1964 to 2018 and were published from 1992 until 2019. 17 studies with a total number of 249 CPs were performed for post-pancreatectomy complications. Mortality rate was 44.5% (111 out of 249). Morbidity rate was (72.6%). 12 studies with 225 CPs were performed for isolated local recurrence after initial resection with a morbidity rate of 21.5% and 0% mortality rate in the early postoperative period. Two studies with a total number of 12 patients reported CP as a treatment option for recurrent neuroendocrine neoplasms. The mortality in those studies was 8% (1/12) and the mean morbidity rate was 58.3% (7/12). Finally, CP for refractory chronic pancreatitis was presented in one study with morbidity and mortality rates of 19% and 0%, respectively.
CONCLUSION
Completion pancreatectomy is a distinct treatment option for various pathologies. Morbidity and mortality rates depend on the indications of performing CP, the status performance of the patients and whether the operation is performed electively or urgently
Topics: Humans; Pancreatectomy; Pancreatic Neoplasms; Neoplasm Recurrence, Local; Pancreas; Pancreatitis, Chronic; Retrospective Studies; Postoperative Complications
PubMed: 37295804
DOI: 10.1177/00031348231183121 -
Neuro-oncology Nov 2023The international, multicenter registry LOGGIC Core BioClinical Data Bank aims to enhance the understanding of tumor biology in pediatric low-grade glioma (pLGG) and...
BACKGROUND
The international, multicenter registry LOGGIC Core BioClinical Data Bank aims to enhance the understanding of tumor biology in pediatric low-grade glioma (pLGG) and provide clinical and molecular data to support treatment decisions and interventional trial participation. Hence, the question arises whether implementation of RNA sequencing (RNA-Seq) using fresh frozen (FrFr) tumor tissue in addition to gene panel and DNA methylation analysis improves diagnostic accuracy and provides additional clinical benefit.
METHODS
Analysis of patients aged 0 to 21 years, enrolled in Germany between April 2019 and February 2021, and for whom FrFr tissue was available. Central reference histopathology, immunohistochemistry, 850k DNA methylation analysis, gene panel sequencing, and RNA-Seq were performed.
RESULTS
FrFr tissue was available in 178/379 enrolled cases. RNA-Seq was performed on 125 of these samples. We confirmed KIAA1549::BRAF-fusion (n = 71), BRAF V600E-mutation (n = 12), and alterations in FGFR1 (n = 14) as the most frequent alterations, among other common molecular drivers (n = 12). N = 16 cases (13%) presented rare gene fusions (eg, TPM3::NTRK1, EWSR1::VGLL1, SH3PXD2A::HTRA1, PDGFB::LRP1, GOPC::ROS1). In n = 27 cases (22%), RNA-Seq detected a driver alteration not otherwise identified (22/27 actionable). The rate of driver alteration detection was hereby increased from 75% to 97%. Furthermore, FGFR1 internal tandem duplications (n = 6) were only detected by RNA-Seq using current bioinformatics pipelines, leading to a change in analysis protocols.
CONCLUSIONS
The addition of RNA-Seq to current diagnostic methods improves diagnostic accuracy, making precision oncology treatments (MEKi/RAFi/ERKi/NTRKi/FGFRi/ROSi) more accessible. We propose to include RNA-Seq as part of routine diagnostics for all pLGG patients, especially when no common pLGG alteration was identified.
Topics: Child; Humans; Proto-Oncogene Proteins B-raf; Pathology, Molecular; Protein-Tyrosine Kinases; RNA-Seq; Proto-Oncogene Proteins; Precision Medicine; Glioma; DNA-Binding Proteins; Transcription Factors
PubMed: 37075810
DOI: 10.1093/neuonc/noad078 -
Histopathology Jul 2024Deep learning holds immense potential for histopathology, automating tasks that are simple for expert pathologists and revealing novel biology for tasks that were...
AIMS
Deep learning holds immense potential for histopathology, automating tasks that are simple for expert pathologists and revealing novel biology for tasks that were previously considered difficult or impossible to solve by eye alone. However, the extent to which the visual strategies learned by deep learning models in histopathological analysis are trustworthy or not has yet to be systematically analysed. Here, we systematically evaluate deep neural networks (DNNs) trained for histopathological analysis in order to understand if their learned strategies are trustworthy or deceptive.
METHODS AND RESULTS
We trained a variety of DNNs on a novel data set of 221 whole-slide images (WSIs) from lung adenocarcinoma patients, and evaluated their effectiveness at (1) molecular profiling of KRAS versus EGFR mutations, (2) determining the primary tissue of a tumour and (3) tumour detection. While DNNs achieved above-chance performance on molecular profiling, they did so by exploiting correlations between histological subtypes and mutations, and failed to generalise to a challenging test set obtained through laser capture microdissection (LCM). In contrast, DNNs learned robust and trustworthy strategies for determining the primary tissue of a tumour as well as detecting and localising tumours in tissue.
CONCLUSIONS
Our work demonstrates that DNNs hold immense promise for aiding pathologists in analysing tissue. However, they are also capable of achieving seemingly strong performance by learning deceptive strategies that leverage spurious correlations, and are ultimately unsuitable for research or clinical work. The framework we propose for model evaluation and interpretation is an important step towards developing reliable automated systems for histopathological analysis.
Topics: Humans; Deep Learning; Lung Neoplasms; Adenocarcinoma of Lung; Neural Networks, Computer; Mutation
PubMed: 38556922
DOI: 10.1111/his.15180 -
Translational Vision Science &... Aug 2023To develop a feline model of acute Acanthamoeba keratitis using methods that replicate natural routes of infection transmission.
PURPOSE
To develop a feline model of acute Acanthamoeba keratitis using methods that replicate natural routes of infection transmission.
METHODS
Corneal Acanthamoeba castellanii inoculation was performed by three methods: topical inoculation with Acanthamoeba solution following corneal abrasion, placement of a contaminated contact lens for 7 days, and placement of a contaminated contact lens for 7 days following corneal abrasion. Sham inoculations with parasite-free medium and sterile contact lenses were also performed. Cats were monitored by ocular examination and in vivo corneal confocal microscopy for 21 days post-inoculation. Corneal samples were collected at intervals for microbiologic assessment, histopathology, and immunohistochemistry.
RESULTS
All cats in the corneal abrasion groups developed clinical keratitis. Clinical ocular disease was inconsistently detected in cats from the contaminated contact lens only group. Initial corneal lesions were characterized by multifocal epithelial leukocyte infiltrates. Ocular lesions progressed to corneal epithelial ulceration and diffuse stromal inflammation. After 14 days, corneal ulcerations resolved, and stromal inflammation consolidated into multifocal subepithelial and stromal infiltrates. Corneal amoebae were detected by culture, in vivo confocal microscopy, histopathology, and immunohistochemistry in cats with keratitis. Neutrophilic and lymphocytic keratoconjunctivitis with lymphoplasmacytic anterior uveitis were identified by histopathology. Coinfection with aerobic bacteria was detected in some, but not all, cats with keratitis. Ocular disease was not detected in the sham inoculation groups.
CONCLUSIONS
Feline Acanthamoeba keratitis is experimentally transmissible by contaminated contact lenses and topical inoculation following corneal epithelial trauma.
TRANSLATIONAL RELEVANCE
Experimentally induced acute Acanthamoeba keratitis in cats is clinically and histopathologically similar to its human counterpart.
Topics: Cats; Animals; Humans; Acanthamoeba Keratitis; Acanthamoeba castellanii; Cornea; Corneal Injuries; Inflammation
PubMed: 37566398
DOI: 10.1167/tvst.12.8.10 -
The American Journal of Surgical... Jan 2024Diagnostic classification of soft tissue tumors is based on histology, immunohistochemistry, genetic findings, and radiologic and clinical correlations. Recently, a...
Diagnostic classification of soft tissue tumors is based on histology, immunohistochemistry, genetic findings, and radiologic and clinical correlations. Recently, a sarcoma DNA methylation classifier was developed, covering 62 soft tissue and bone tumor entities. The classifier is based on large-scale analysis of methylation sites across the genome. It includes DNA copy number analysis and determines O 6 methylguanine DNA methyl-transferase methylation status. In this study, we evaluated 619 well-studied soft tissue and bone tumors with the sarcoma classifier. Problem cases and typical examples of different entities were included. The classifier had high sensitivity and specificity for fusion sarcomas: Ewing, synovial, CIC -rearranged, and BCOR -rearranged. It also performed well for leiomyosarcoma, malignant peripheral nerve sheath tumors (MPNST), and malignant vascular tumors. There was low sensitivity for diagnoses of desmoid fibromatosis, neurofibroma, and schwannoma. Low specificity of matches was observed for angiomatoid fibrous histiocytoma, inflammatory myofibroblastic tumor, Langerhans histiocytosis, schwannoma, undifferentiated sarcoma, and well-differentiated/dedifferentiated liposarcoma. Diagnosis of lipomatous tumors was greatly assisted by the detection of MDM2 amplification and RB1 loss in the copy plot. The classifier helped to establish diagnoses for KIT-negative gastrointestinal stromal tumors, MPNSTs with unusual immunophenotypes, and undifferentiated melanomas. O 6 methylguanine DNA methyl-transferase methylation was infrequent and most common in melanomas (35%), MPNSTs (11%), and undifferentiated sarcomas (11%). The Sarcoma Methylation Classifier will likely evolve with the addition of new entities and refinement of the present methylation classes. The classifier may also help to define new entities and give new insight into the interrelationships of sarcomas.
Topics: Humans; DNA Methylation; Melanoma; Pathology, Surgical; Sarcoma; Liposarcoma; Soft Tissue Neoplasms; Neurilemmoma; Neurofibrosarcoma; Transferases; DNA; Biomarkers, Tumor
PubMed: 37921028
DOI: 10.1097/PAS.0000000000002138 -
PLoS Pathogens Aug 2023Most humans have a lifelong imperceptible BK Polyomavirus (BKPyV) infection in epithelial cells lining the reno-urinary tract. In kidney transplant recipients,...
Most humans have a lifelong imperceptible BK Polyomavirus (BKPyV) infection in epithelial cells lining the reno-urinary tract. In kidney transplant recipients, unrestricted high-level replication of donor-derived BKPyV in the allograft underlies polyomavirus-associated nephropathy, a condition with massive epithelial cell loss and inflammation causing premature allograft failure. There is limited understanding on how BKPyV disseminates throughout the reno-urinary tract and sometimes causes kidney damage. Tubule epithelial cells are tightly connected and have unique apical and basolateral membrane domains with highly specialized functions but all in vitro BKPyV studies have been performed in non-polarized cells. We therefore generated a polarized cell model of primary renal proximal tubule epithelial cells (RPTECs) and characterized BKPyV entry and release. After 8 days on permeable inserts, RPTECs demonstrated apico-basal polarity. BKPyV entry was most efficient via the apical membrane, that in vivo faces the tubular lumen, and depended on sialic acids. Progeny release started between 48 and 58 hours post-infection (hpi), and was exclusively detected in the apical compartment. From 72 hpi, cell lysis and detachment gradually increased but cells were mainly shed by extrusion and the barrier function was therefore maintained. The decoy-like cells were BKPyV infected and could transmit BKPyV to uninfected cells. By 120 hpi, the epithelial barrier was disrupted by severe cytopathic effects, and BKPyV entered the basolateral compartment mimicking the interstitial space. Addition of BKPyV-specific neutralizing antibodies to this compartment inhibited new infections. Taken together, we propose that during in vivo low-level BKPyV replication, BKPyV disseminates inside the tubular system, thereby causing minimal damage and delaying immune detection. However, in kidney transplant recipients lacking a well-functioning immune system, replication in the allograft will progress and eventually cause denudation of the basement membrane, leading to an increased number of decoy cells, high-level BKPyV-DNAuria and DNAemia, the latter a marker of allograft damage.
Topics: Humans; Cytology; BK Virus; Polyomavirus; Kidney; Epithelial Cells; Polyomavirus Infections
PubMed: 37639485
DOI: 10.1371/journal.ppat.1011622