Search

After smallpox was eradicated worldwide in 1980 and routine smallpox vaccination subsequently ceased, monkeypox virus (MPXV) emerged as the most consequential orthopoxvirus for public health (1). The genetic clades of [...]

Context.--Nucleophosmin 1 (NPM1) mutations affect 20% to 30% of all acute myeloid leukemia (AML) patients; several methods are employed to analyze NPM1 mutations, each of them with its advantages and limitations. Objective.--To compare 3 nonsequencing protocols capable of detecting the main NPM1 mutations and to evaluate nuclear morphometric analysis (NMA) as an alternative to cuplike blast detection. Design.--We selected multiparameter flow cytometry (MFC), amplification refractory mutation system-polymerase chain reaction (ARMS-PCR), and a quantitative PCR (qPCR) kit to identify NPM1 mutations in AML patients at diagnosis. We also evaluated the presence of cuplike blasts and assessed nuclear morphometry using NMA. Results.--MFC appears as a screening method for NPM1 mutations because of its lower specificity. ARMS-PCR demonstrated specificity similar to that of the qPCR kit, although it was more laborious. qPCR testing, conversely, is relatively fast and easy to standardize. Of these methods, qPCR was the only one capable of identifying the type of NPM1 mutation. With regard to morphology, NMA could be used as an alternative for the evaluation of cuplike blasts in AML smears. Conclusions.--qPCR appears to be the best option to identify NPM1 mutations, with ARMS-PCR representing a cheaper alternative. MFC may be used as a screening method, in which results falling within and above the gray zone should be confirmed by molecular testing. (Arch Pathol Lab Med. 2023;147:701-709; doi: 10.5858/arpa.2021-0601-OA), Mutations in the nucleophosmin 1 (NPM1) gene are one of the most common mutations found in acute myeloid leukemia (AML) and affect approximately 30% of patients with primary AML. When [...]

Legionellosis is caused by the gram-negative bacterium Legionella. This infection is predominantly the consequence of an environmental exposure to legionellae, which are ubiquitous in water and moist soil ecosystems. Incidence [...]

Bartonella spp. are fastidious, gram-negative intracellular bacteria that are transmitted to humans by insect vectors. The genus includes 12 species associated with human infection: B. henselae, B. quintana, B. bacilliformis, [...]

Diffuse large B cell lymphoma (DLBCL) often develops resistance and/or relapses in response to immunochemotherapy. Epigenetic modifiers are frequently mutated in DLBCL, i.e., the lysine (histone) acetyltransferases CREBBP and EP300. Mutations in CBP/p300 can prevent the proper acetylation and activation of (i) enhancer sequences of genes required for essential functions (e.g., germinal center exit and differentiation) and (ii) the tumor suppressor p53. Based on evidence that omega-3 fatty acids ([omega]-3 FAs) affect histone acetylation in various cancers, we investigated whether [omega]-3 FA docosahexaenoic acid (DHA) could modify levels of histone and p53 acetylation in three DLBCL cell lines (at different CREBBP/EP300 mutational status) versus normal B cells. Exposure to DHA at clinically attainable doses was shown to significantly alter the genome-wide levels of histone post-translational modifications in a cell-line-dependent and dose-dependent manner. Although histone acetylation did not increase uniformly as initially expected, levels of p53 acetylation increased consistently. Quantitative reverse transcription polymerase chain reaction results revealed significant changes in expression of multiple genes, including increased expression of CREBBP and of PRDM1 (required for differentiation into plasma cells or memory B cells). Taken together, our results provide (to our knowledge) the first characterization of the epigenetic effects of [omega]-3 FAs in DLBCL. Key words: diffuse large B-cell lymphoma, genetics, epigenetics, omega-3 fatty acid, acetylation, Introduction Diffuse large B cell lymphoma (DLBCL) is the most common type of lymphoma (Morton et al. 2006; Freedman and Aster 2022), with an incidence rate of 5.6 per 100 [...]

Human granulocytic anaplasmosis (HGA) is a tickborne infection caused by the intracellular bacterium Anaplasma phagocytophilum (1), an emerging pathogen in North America (2-5). HGA can manifest as a subclinical infection; [...]

Reports of the expansion of the malaria vector Anopheles stephensi mosquito (1-6) are increasing, intensifying the threat of urban malaria (7). The gradual southward expansion of this species has been [...]

African horse sickness (AHS) is a fatal vector-borne disease affecting all species of equids. The disease has major economic consequences for the equine industry. The World Organisation for Animal Health [...]

A global outbreak of mpox was detected in May 2022 and declared a Public Health Emergency of International Concern on July 23 (1). We investigated how monkeypox virus (MPXV) cycle [...]

In May 2022, an unusually high number of monkeypox cases were reported in countries in western Europe and North America; by May 29, 2022, 257 laboratory-confirmed infections were reported from [...]

Context.--Reverse transcription-polymerase chain reaction (RT-PCR) is the standard method of diagnosing COVID-19. An inconclusive test result occurs when 1 RT-PCR target is positive for SARS-CoV-2 and 1 RT-PCR target is negative for SARS-CoV-2 within the same sample. An inconclusive result generally requires retesting. One reason why a sample may yield an inconclusive result is that one target is at a higher concentration than another target. Objective.--To understand the role of subgenomic RNA transcripts in discordant results from RT-PCR tests for COVID-19. Design.--A panel of 6 droplet digital PCR assays was designed to quantify the ORF1, E-gene, and N-gene of SARS-CoV-2. This panel was used to quantify viral cultures of SARS-CoV-2 that were harvested during the eclipse phase and at peak infectivity. Eleven clinical nasopharyngeal swabs were also tested with this panel. Results.--In culture, infected cells showed higher Ngene/ORF1 copy ratios than culture supernatants. The same trends in the relative abundance of copies across different targets observed in infected cells were observed in clinical samples, although trends were more pronounced in infected cells. Conclusions.--This study showed that a greater copy number of N-gene relative to E-gene and ORF1 transcripts could potentially explain inconclusive results for some RTPCR tests on low viral load samples. The use of N-gene RTPCR target(s) as opposed to ORF1 targets for routine testing is supported by these data., Reverse transcriptase-polymerase chain reaction (RTPCR) is the standard method of diagnosing COVID19 in a laboratory. (1-4) RT-PCR tests for COVID-19 qualitatively detect SARS-CoV-2 RNA from patient samples. (1-4) SARS-CoV-2 is [...]

Context.--Studies of lungs in patients with COVID-19 have focused on early findings. Objective.--To systematically study histopathologic and imaging features and presence of SARS-CoV-2 RNA in lung tissue from patients in later stages of COVID-19. Design.--Autopsies, explants, surgical lung biopsies, transbronchial biopsies, cryobiopsies, and needle biopsies from patients with COVID-19 whose onset of symptoms/ confirmed diagnosis was more than 28 days before the procedure were studied. Available images were reviewed. Reverse transcription droplet digital polymerase chain reaction for SARS-CoV-2 RNA was performed on lung tissue. Results.--Of 44 specimens (43 patients; median age, 59.3 years; 26 [60.5%] male) features of acute lung injury (ALI) were seen in 39 (88.6%), predominantly organizing pneumonia and diffuse alveolar damage, up to 298 days after onset of COVID-19. Fibrotic changes were found in 33 specimens (75%), most commonly fibrotic diffuse alveolar damage (n = 22) and cicatricial organizing pneumonia (n = 12). Time between acquiring COVID-19 and specimen was shorter in patients with diffuse ALI (median, 61.5 days) compared with patients with focal (140 days) or no AlI (130 days) (P =.009). Sixteen (of 20; 80%) SARS-CoV-2 reverse transcription droplet digital polymerase chain reaction tests were positive, up to 174 days after COVID-19 onset. Time between COVID-19 onset and most recent computed tomography in patients with consolidation on imaging was shorter (median, 43.0 days) versus in patients without consolidation (87.5 days; P =.02). Reticulations were associated with longer time to computed tomography after COVID-19 onset (median, 82 versus 23.5 days; P =.006). Conclusions.--ALI and SARS-CoV-2 RNA can be detected in patients with COVID-19 for many months. ALI may evolve into fibrotic interstitial lung disease., Coronavirus disease 2019 (COVID-19) is a viral infection caused by SARS-CoV-2. More than 235 million people have been infected globally, with a death burden in excess of 4.8 million since [...]

* Context.--Associations between granulomatous lobular mastitis (GLM) and Corynebacterium kroppenstedtii have been reported since 2002, but large-scale studies to assess the actual prevalence of this bacterium in GLM have not been performed. Objective.--To assess the prevalence of C kroppenstedtii in GLM using real-time polymerase chain reaction and Sanger sequencing. Design.--We analyzed formalin-fixed, paraffin-embedded tissues from 67 cases of GLM by sequential DNA amplification and sequencing to assess the rate of C kroppenstedtii detection in GLM. A retrospective analysis including patient demographics, history of pregnancy and lactation, clinical signs and symptoms, radiographic findings, histologic pattern, Gram stain results, and microbial cultures was performed on 67 cases of GLM. In addition, 10 cases of nongranulomatous breast abscess were included as controls. Results.--C kroppenstedtii 16S rRNA SYBR real-time polymerase chain reaction was positive on formalin-fixed, paraffin-embedded tissues from 46 of 67 (68.7%) GLM cases, while all control cases were negative. Among the positive cases, the majority showed features of cystic neutrophilic granulomatous mastitis. Conclusions.--C kroppenstedtii was highly prevalent in GLM cases and was not found to be associated with nongranulomatous breast abscess in our study (P < .001)., Granulomatous lobular mastitis (GLM) is an uncommon benign, inflammatory disease of the breast first described in 1972 by Kessler and Wolloch (1) that characteristically affects women of childbearing age with [...]

Context.--The gold standard test to identify the presence of SARS-CoV-2 in COVID-19 patients is the real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR), but inconclusive data and false-positive diagnosis remain the major problem of this approach. Objective.--To compare the fitness of 2 primer sets to the SARS-CoV-2 nucleocapsid phosphoprotein gene (NP) in the molecular diagnosis of COVID-19, we verified the inconclusive data and confidence of high cycle threshold (Ct) values in SARS-CoV-2 detection. Design.--The 970 patient samples were tested by using United States Centers for Disease Control and Prevention protocol. We compared the fitness of 2 primer sets to 2 different regions of the NP gene. In addition, we checked the consistency of positive samples with high Ct values by retesting extracted SARS-CoV-2 RNA or by second testing of patients. Results.--N1 and N2 displayed similar fitness during testing, with no differences between Ct values. Then, we verified security range Ct values related to positive diagnostics, with Ct values above 34 failing in 21 of 32 cases (65.6%) after retesting of samples. The patient samples with Ct values above 34.89 that were doubly positive revealed a low sensitivity (52.4%) and specificity (63.6%) of the test in samples with Ct values above 34. Conclusions.--It is safe to use 1 primer set for the NP gene to identify SARS-CoV-2 in samples. However, samples with high Ct values may be considered inconclusive and retested to avoid false-positive diagnosis. (Arch Pathol Lab Med. 2022;146:272-277; doi: 10.5858/arpa.2021-0423-SA), Demands for molecular diagnosis to test COVID-19 are fast growing around the world, and costs and efficiency of the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) technique have been in check. [...]

* Context.--The FilmArray Meningitis/Encephalitis (ME) panel is the first US Food and Drug Administration-cleared multiplex polymerase chain reaction panel for the detection of central nervous system infections. While the assay's [...]

* Context.--Bone and soft tissue tumors are heterogeneous, diagnostically challenging, and often defined by gene fusions. Objective.--To present our experience using a custom 34-gene targeted sequencing fusion panel. Design.--Total nucleic acid extracted from formalin-fixed, paraffin-embedded (FFPE) tumor specimens was subjected to open-ended, nested anchored multiplex polymerase chain reaction and enrichment of 34 gene targets, thus enabling detection of known and novel fusion partners. Results.--During a 12-month period, 147 patients were tested as part of routine clinical care. Tumor percentage ranged from 10% to 100% and turnaround time ranged from 3 to 15 (median, 7.9) days. The most common diagnostic groups were small round blue cell tumors, tumors of uncertain differentiation, fibroblastic/myofibroblastic tumors, and adipocytic tumors. In-frame fusion transcripts were identified in 64 of 142 cases sequenced (45%): in 62 cases, the detection of a disease-defining fusion confirmed the morphologic impression; in 2 cases, a germline TFG-GPR128 polymorphic fusion variant was detected. Several genes in the panel partnered with multiple fusion partners specific for different diagnoses, for example, EWSR1, NR4A3, FUS, NCOA2, and TFE3. Interesting examples are presented to highlight how fusion detection or lack thereof was instrumental in establishing accurate diagnoses. Novel fusion partners were detected for 2 cases of solid aneurysmal bone cysts (PTBP1-USP6, SLC38A2-USP6). Conclusions.--Multiplex detection of fusions in total nucleic acid purified from FFPE specimens facilitates diagnosis of bone and soft tissue tumors. This technology is particularly useful for morphologically challenging entities and in the absence of prior knowledge of fusion partners, and has the potential to discover novel fusion partners. (Arch Pathol Lab Med. 2021;145:851-863; doi: 10.5858/arpa.2020-0336-OA), Gene fusions occur frequently in bone and soft tissue (BST) neoplasms and, less frequently, in other kinds of solid tumors. (1-3) The observation of these fusions in patient specimens can [...]

An outbreak of pneumonia of unknown etiology in Wuhan, China, was reported to the World Health Organization on December 31, 2019 (1). Researchers determined that the illness, later known as [...]

Rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential to prevent viral dissemination. Rapid antigen tests (RATs) have recently been approved and are now widely used in [...]

A robust surveillance system for early identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) is of critical public health value. VOCs have demonstrated in vitro [...]

Context.--The increasing use of large panel next-generation sequencing technologies in clinical settings has facilitated the identification of pan-cancer biomarkers, which can be diagnostic, prognostic, predictive, or most importantly, actionable. Objective.--To discuss recently approved and emerging pan-cancer and multihistology biomarkers as well as testing methodologies. Data Sources.--The US Food and Drug Administration approval documents, National Comprehensive Cancer Network guidelines, literature, and authors' own publications. Conclusions.--Since 2017, the US Food and Drug Administration has approved genotype-directed therapies for pan-cancer biomarkers, including microsatellite instability, neurotrophic receptor kinases fusions, and high-tumor mutation burden. Both the importance and rarity of these biomarkers have increased the prevalence of genomic profiling across solid malignancies. As an integral part of the management team of patients with advanced cancer, pathologists need to be aware of these emerging biomarkers, the therapies for which they determine eligibility, and the strengths and pitfalls of the available clinical assays. (Arch Pathol Lab Med. 2021;145:692-698; doi: 10.5858/arpa.2020-0513-RA, Massively parallel or next-generation sequencing (NGS) of large panels of genes in all tumor types has amplified our knowledge about the prevalence of certain oncogenic alterations and played a large [...]

* Context.--Coronavirus disease 2019 (COVID-19) has been shown to have effects outside of the respiratory system. Placental pathology in the setting of maternal severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) infection remains a topic of great interest because earlier studies have shown mixed results. Objective.--To ascertain whether maternal SARS-CoV-2 infection is associated with any specific placental histopathology, and to evaluate the virus's propensity for direct placental involvement. Design.--Placentas from 65 women with polymerase chain reaction-proven SARS-CoV-2 infection underwent histologic evaluation using Amsterdam consensus group criteria and terminology. Another 85 placentas from women without SARS-CoV-2 constituted the negative control group. A total of 64 of the placentas from the SARS-CoV-2-positive group underwent immunohistochemical staining for SARS-CoV-2 nucleocapsid protein. Results.--Pathologic findings were divided into maternal vascular malperfusion, fetal vascular malperfusion, chronic inflammatory lesions, amniotic fluid infection sequence, increased perivillous fibrin, intervillous thrombi, increased subchorionic fibrin, meconium-laden macrophages (MLMs) within fetal membranes, and chorangiosis. There was no statistically significant difference in prevalence of any specific placental histopathology between the SARS-CoV2-positive and SARS-CoV-2-negative groups. There was no immunohistochemical evidence of SARS-CoV-2 virus in any of the 64 placentas that underwent staining for viral nucleocapsid protein. Conclusions.--Our study results and a literature review suggest that there is no characteristic histopathology in most placentas from women with SARS-CoV-2 infection. Likewise, direct placental involvement by SARS-CoV-2 is a rare event. (Arch Pathol Lab Med. 2021;145:648-656; doi: 10.5858/arpa.2020-0793-SA, Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). (1) Significant infection often manifests as acute respiratory distress syndrome, reflecting the virus's predominant [...]

This study examined the hypothesis that the microRNA miR-138-5p reduces the osteodifferentiation of human bone mesenchymal stem cells (hBMSCs) by downregulating the expression of forkhead box C1 (FOXC1). For this, hBMSCs were separated from bone marrow and osteogenic induction medium was added to stimulate osteogenic differentiation. Flow cytometric analysis was applied to evaluate the expression of cell-surface antigens associated with hBMSCs, including CD29, CD44, CD90, CD45, and CD34. qRT-PCR assays and Western blot assays were used to measure the mRNA and protein expression of miR-138-5p, osteocalcin, runt-related transcription factor 2, bone sialoprotein, alkaline phosphatase (ALP), and FOXC1. ALP staining assays and Alizarin Red staining (ARS) assays were used to confirm osteogenic differentiation. We used a luciferase assay to test the interaction between miR-138-5p and FOXC1. We demonstrated that miR-138-5p is downregulated in osteogenic differentiated hBMSCs. Further, overexpression of miR-138-5p reduced the expression of markers for osteodifferentiation, ALP activity, and ARS activity. Furthermore, we showed that FOXC1 is a downstream target gene of miR-138-5p, and that knockdown of miR-138-5p improves the osteogenesis differentiation of hBMSCs by upregulating FOXC1. The results from this study indicate miR-138-5p as a new target for osteogenic differentiation of hBMSCs and the treatment of bone defects. Key words: miR-138-5p, osteogenic differentiation, FOXC1, hBMSCs. Cette étude visait à vérifier l'hypothèse selon laquelle le miR-138-5p devrait réduire la différenciation ostéogénique des cellules souches mésenchymateuses osseuses humaines (CSMh) par la régulation négative de [beaucoup moins que] forkhead box C1 [beaucoup plus grand que] (FOXC1). Les CSMh ont été séparées de la moelle osseuse et un milieu d'induction ostéogénique a été ajouté pour stimuler la différenciation ostéogénique. L'analyseen cytométriede flux a été utilisée pour évaluer l'expression des antigènes cellulaires de surface associés aux CSMh, dont les CD29, CD44, CD90, CD45 et CD34. La qRT-PCR et le transfert Western ont été utilisés pour mesurer l'expression de l'ARNm et des protéines miR-138-5p, OCN, RUNX2, BSP, PAL et FOXC1. La coloration de la phosphatase alcaline (PAL) et la coloration au rouge d'alizarine (ARS) ont été réalisés pour confirmer la différenciation ostéogénique. Le dosage de la luciférase a été utilisé pour tester l'interaction entre le miR-138-5p et FOXC1. Les auteurs ont démontré que le miR-138-5p est régulé à la baisse dans les CSMh à la suite de la différenciation ostéogénique. En outre, la surexpression du miR-138-5p diminuait l'expression des marqueurs de la différenciation ostéogénique, l'activité de la PAL et l'activité de l'ARS. De plus, ils ont révélé que FOXC1 était un gène cible en aval du miR-138-5p et que le knockdown du miR-138-5p améliorait la différenciation ostéogénique des CSMh en augmentant la régulation à la hausse de FOXC1. Cette étude suggère que le miR-138-5p pourrait être une nouvelle cible pour la différenciation ostéogénique des CSMh et le traitement des défauts osseux. [Traduit par la Rédaction] Mots-clés: miR-138-5p, différenciation ostéogénique, FOXC1, CSMh., Introduction Large segmental bone defects caused by comminuted fracture, tumor resection, or osteomyelitis remain significant problems in the context of surgery (Wu et al. 2018). Autograft is the most commonly [...]

Suppressing infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will probably require the rapid identification and isolation of individuals infected with the virus on an ongoing basis. Reverse-transcription polymerase chain reaction (RT-PCR) tests are accurate but costly, which makes the regular testing of every individual expensive. These costs are a challenge for all countries around the world, but particularly for low-to-middle-income countries. Cost reductions can be achieved by pooling (or combining) subsamples and testing them in groups.sup.1-7. A balance must be struck between increasing the group size and retaining test sensitivity, as sample dilution increases the likelihood of false-negative test results for individuals with a low viral load in the sampled region at the time of the test.sup.8. Similarly, minimizing the number of tests to reduce costs must be balanced against minimizing the time that testing takes, to reduce the spread of the infection. Here we propose an algorithm for pooling subsamples based on the geometry of a hypercube that, at low prevalence, accurately identifies individuals infected with SARS-CoV-2 in a small number of tests and few rounds of testing. We discuss the optimal group size and explain why, given the highly infectious nature of the disease, largely parallel searches are preferred. We report proof-of-concept experiments in which a positive subsample was detected even when diluted 100-fold with negative subsamples (compared with 30-48-fold dilutions described in previous studies.sup.9-11). We quantify the loss of sensitivity due to dilution and discuss how it may be mitigated by the frequent re-testing of groups, for example. With the use of these methods, the cost of mass testing could be reduced by a large factor. At low prevalence, the costs decrease in rough proportion to the prevalence. Field trials of our approach are under way in Rwanda and South Africa. The use of group testing on a massive scale to monitor infection rates closely and continually in a population, along with the rapid and effective isolation of people with SARS-CoV-2 infections, provides a promising pathway towards the long-term control of coronavirus disease 2019 (COVID-19). A mathematical algorithm for population-wide screening of SARS-CoV-2 infections using pooled parallel RT-PCR tests requires considerably fewer tests than individual testing procedures and has minimal delays in the identification of individuals infected with SARS-CoV-2., Author(s): Leon Mutesa [sup.1] [sup.2] , Pacifique Ndishimye [sup.2] [sup.3] , Yvan Butera [sup.1] [sup.2] , Jacob Souopgui [sup.1] [sup.2] [sup.4] , Annette Uwineza [sup.1] [sup.2] , Robert Rutayisire [sup.1] [...]

Severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) is causing a global pandemic and affecting global health and the world economy. Virus RNA might be detectable by reverse transcription PCR [...]