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[Natural pathogenicity for man of an antigenic variant of Soldado virus from Morocco (author's transl)].

Pathogenicity of Soldado virus was clearly established in the past for seabirds but remained questionable for man. In a scientist, repeatedly bitten by Ornithodoros (A.) maritimus larvae at Essaouira (Morocco), the association of fever of unknown origin and of neutralizing antibody against an antigenic variant of Soldado virus isolated from the same place, lead to the conclusion that this virus may act as a pathogen for man. Epidemiological implications of such an observation are briefly discussed.

Adult↗

PubMed2006

Detection of exon deletions within an entire gene (CFTR) by relative quantification on the LightCycler.

BACKGROUND: Cystic fibrosis (CF) is associated with at least 1 pathogen point sequence variant on each CFTR allele. Some symptomatic patients, however, have only 1 detectable pathogen sequence variant and carry, on the other allele, a large deletion that is not detected by conventional screening methods. METHODS: For relative quantitative real-time PCR detection of large deletions in the CFTR gene, we designed DNA-specific primers for each exon of the gene and primers for a reference gene (beta2-microglobulin). For PCR we used a LightCycler system (Roche) and calculated the gene-dosage ratio of CFTR to beta2-microglobulin. We tested the method by screening all 27 exons in 3 healthy individuals and 2 patients with only 1 pathogen sequence variant. We then performed specific deletion screenings in 10 CF patients with known large deletions and a blinded analysis in which we screened 24 individuals for large deletions by testing 8 of 27 exons. RESULTS: None of the ratios for control samples were false positive (for deletions or duplications); moreover, for all samples from patients with known large deletions, the calculated ratios for deleted exons were close to 0.5. In addition, the results from the blinded analysis demonstrated that our method can also be used for the screening of single individuals. CONCLUSIONS: The LightCycler assay allows reliable and rapid screening for large deletions in the CFTR gene and detects the copy number of all 27 exons.

Cystic Fibrosis↗

PubMed2026

Genotype-structure-phenotype correlations define divergent natural history in early-onset spastic paraplegia type 4.

Hereditary spastic paraplegia type 4 (SPG4), caused by variants in SPAST, is the most common form of HSP and exhibits a remarkable phenotypic heterogeneity ranging from late-onset pure presentations to severe, early-onset complex disease. Robust genotype-phenotype correlations and detailed natural history data are lacking, limiting clinical trial readiness. We analyzed 206 patients with genetically confirmed SPG4 enrolled across seven international centers, complemented by high-quality literature-derived cases. Deep phenotyping included standardized motor scales, spasticity ratings, developmental milestones, and patient-reported outcomes. We developed an extended essentiality-mapping framework to classify SPAST missense variants by integrating in silico pathogenicity predictions, evolutionary constraint, physicochemical residue connectivity, and variant enrichment within the human spastin hexamer structure. Plasma neurofilament light chain (pNfL) using was quantified using Simoa in 26 patients and 101 controls. We identified 136 distinct SPAST variants, including 10 novel variants. Variant class segregated strongly by inheritance, with de novo cases enriched for missense variants and inherited cases showing a variety of variant classes with enrichment for truncating variants. Longitudinal analysis revealed two latent trajectories: a rapidly progressive severe subgroup enriched for de novo missense variants, and a biphasic moderate subgroup enriched for inherited truncating variants. Patient stratification integrating spastin essentiality mapping (missense variants affecting essential, neutral, or context-dependent residues) with established genetic modifiers (biallelic pathogenic variants or modifier variants in trans) classified patients into predicted severe and moderate subgroups with divergent age at onset and clinical disease progression. The severe subgroup showed early developmental delays, rapid loss of ambulation, and declining quality of life, while the moderate subgroup displayed delayed but accelerating disease progression. pNfL levels were elevated in both subgroups, most pronounced in severe early disease. This study provides the most detailed natural history of SPG4 to date and introduces a biologically informed stratification framework that links variant class and location to divergent clinical trajectories. These data establish clinically meaningful benchmarks and offer a genotype-based framework to improve anticipatory care and optimize trial design for SPG4.

SPAST↗

PubMed2026

Characterization of a series of patients with GNE-related thrombocytopenia: insights into pathogenesis, diagnosis, and treatment.

BACKGROUND: GNE-related thrombocytopenia (GNE-RT) is a very rare disorder caused by biallelic variants in GNE, which encodes a key enzyme in sialic acid biosynthesis. Patients usually present with severe thrombocytopenia and excessive bleeding. Knowledge of this condition remains limited. There are no recognized diagnostic tests for the diagnosis of GNE-RT. A previous study showed reduced platelet half-life as a mechanism of thrombocytopenia; however, it remains unclear whether the sialylation defect also impairs platelet biogenesis. OBJECTIVES: To gain insights into the clinical aspects and platelet biogenesis of GNE-RT. METHODS: We investigated 4 new GNE-RT patients (3 families). A recently standardized flow cytometry assay was used to characterize platelet sialylation. Patients' megakaryocytes were cultured to study megakaryopoiesis and proplatelet formation. A validated 3-dimensional bone marrow model was used to investigate platelet production. RESULTS: We characterized 3 novel GNE variants and demonstrated the pathogenicity of 2 variants of uncertain significance. In all individuals, platelet flow cytometry showed increased RCA-1 and ECL lectin binding and decreased MAL-II binding. Sialylation of serum transferrin showed no clear alterations. Despite the sialylation defect, patients' megakaryocytes showed preserved differentiation, maturation, and proplatelet formation. Ex vivo, megakaryocytes produced a normal number of normal-sized platelets. Two patients received eltrombopag and achieved a durable clinical response (38- and 72-month follow-up). CONCLUSION: The profound megakaryocyte sialylation defect induced by GNE variants does not affect platelet biogenesis. Platelet flow cytometry assessing RCA-1 and MAL-II binding is a reliable, simple assay for diagnosing GNE-RT. Based on a literature review, 55% of GNE-RT patients respond to thrombopoietin mimetics.

GNE gene↗

PubMed2024

Quantitative natural history modeling of HPDL-related disease based on cross-sectional data reveals genotype-phenotype correlations.

PURPOSE: Biallelic HPDL variants have been identified as the cause of a progressive childhood-onset movement disorder, with a broad clinical spectrum from severe neurodevelopmental disorder to juvenile-onset pure hereditary spastic paraplegia type 83. This study aims at delineating the geno- and phenotypic spectra of patients with HPDL-related disease, quantitatively modeling the natural history, and uncovering genotype-phenotype associations. METHODS: A cross-sectional analysis of 90 published and 1 novel case was performed, using a Human-Phenotype-Ontology-based approach. Unsupervised phenotypic clustering was used alongside in silico analyses to identify distinct patient subgroups. RESULTS: The study models the natural history of the HPDL-related disease in a global cohort, clarifying the molecular and phenotypic spectrum and identifying 3 distinct subgroups characterized by differences in onset, clinical trajectories, and survival. It establishes genotype-phenotype associations, showing that the presence of moderately pathogenic missense variants in 1 allele leads to a milder, spastic paraplegic phenotype with later disease onset, whereas biallelic, highly pathogenic missense or truncating variants are associated with a more severe phenotype and reduced life span. CONCLUSION: Quantitative and unbiased natural history modeling in HPDL-related disease reveals significant genotype-phenotype associations, providing a foundation for variant interpretation, anticipatory guidance, and choice of outcome measures in future prospective and functional studies.

Humans↗

PubMed2026

[Analysis of clinical spectrum and genotype characteristics of 9 cases of Fabry disease].

Objective: To investigate the genetic characteristics and clinical phenotypes across different genotypes in patients with Fabry disease. Methods: Clinical data of 9 confirmed FD patients treated from June 2019 to December 2025 at the Affiliated Huai'an No.1 people's Hospital of Nanjing Medical University were retrospectively analyzed. The diagnostic criteria for FD included α-galactosidase A (α-GalA) activity, GLA gene sequencing, globotriaosylsphingosine levels, and renal biopsy findings, supplemented by clinical symptoms and signs. Genetic testing was performed on both the proband and their family members. Proband underwent next-generation sequencing of the GLA gene using the long-range PCR. Family members were verified by conventional PCR combined with Sanger sequencing. Variants were classified according to the 2015 American College of Medical Genetics and Genomics guidelines for sequence variation interpretation. Results: Of the 9 patients, 4 were males and 5 were females. The mean α-Gal A activity was (0.47±0.13) μmol·L-1·h-1 in males and (2.38±0.91) μmol·L-1·h-1 in females. The mean age at diagnosis was (43.0±16.7) years. The main clinical manifestations included renal impairment in 7 cases (proteinuria, chronic kidney disease, or end-stage renal disease), cardiac involvement in 8 cases (myocardial hypertrophy, arrhythmia, etc.), and autonomic nervous system symptoms in 6 cases (hypohidrosis). Pathogenic or likely pathogenic GLA variants were identified in all 9 patients, of which 8 were classified as pathogenic and 1 as a variant of uncertain significance. Three patients underwent family screening: in one case, the variant was possibly inherited from the maternal grandmother; one case was confirmed as a de novo mutation; and in one case, paternal inheritance could not be excluded. Renal biopsy in one patient revealed characteristic myeloid bodies and zebra bodies. Among the 9 patients, 1 received agalsidase α and 8 received agalsidase β, with one case developing infusion-associated reactions after 12 infusions. During the follow-up period, one patient died due to cardiac complications. Conclusions: FD patients exhibit a broad clinical spectrum and diverse genotypes. Atypical presentations should be closely monitored to enable early diagnosis and treatment, thereby improving prognosis.

Humans↗

PubMed2001

Mutations in the TMPRSS3 gene are a rare cause of childhood nonsyndromic deafness in Caucasian patients.

Two loci for nonsyndromic recessive deafness located on chromosome 21q22.3 have previously been reported, DFNB8 and DFNB10. Recently a gene which encodes a transmembrane serine protease, TMPRSS3 or ECHOS1, was found to be responsible for both the DFNB8 and DFNB10 phenotypes. To determine the contribution of TMPRSS3 mutations in the general congenital/childhood nonsyndromic deaf population we performed mutation analysis of the TMPRSS3 gene in 448 unrelated deaf patients from Spain, Italy, Greece, and Australia who did not have the common 35delG GJB2 mutation. From the 896 chromosomes studied we identified two novel pathogenic mutations accounting for four mutant alleles and at least 16 nonpathogenic sequence variants. The pathogenic mutations were a 1-bp deletion resulting in a frameshift and an amino acid substitution in the LDLRA domain of TMPRSS3. From this and another study we estimate the frequency of TMPRSS3 mutations in our sample as 0.45%, and approximately 0.38% in the general Caucasian childhood deaf population. However, TMPRSS3 is still an important contributor to genetic deafness in populations with large consanguineous families.

Amino Acid Sequence↗

PubMed1992

Is any strain of Listeria monocytogenes detected in food a health risk?

Listeria spp. have been isolated from various food items. This fact does not mean in any case a true health risk. A balanced appraisal should be based on quantitative as well as qualitative aspects. Actually, there is still an open debate whether a limited number of Listeria has to be tolerated at least in certain food items. In addition, the pathogenic potency of an isolate may be put into account. Pathogenicity of various Listeria spp. definitely varies. Most Listeria spp., except Listeria monocytogenes, can be regarded as harmless to man. Also, not all strains of L. monocytogenes are pathogenic: rough variants possess only reduced virulence; non-hemolytic mutants have completely lost their pathogenic potency. Furthermore, several other virulence factors may be lost under natural conditions, so that among the majority of hemolytic, pathogenic isolates there may be others which are non-pathogenic or of low virulence only. Unfortunately, these strains actually cannot be recognized and characterized by common laboratory tests, so that animal pathogenicity seems to be the only way to get a final conclusion on the health risk of an isolate of L. monocytogenes from any food. The problem raised by this is which animal test is able to predict a true health risk either for normal hosts or for immunocompromised patients?

Food Microbiology↗

PubMed1991

[Effect of viral structure and replication characteristics on the pathogenesis of infectious bursal disease].

Infectious bursal disease (IBD) is a highly contagious disease of young chickens, which occurs world-wide, and is responsible for severe losses in poultry industries. In birds surviving an acute infection, lymphoid cells in the bursa of Fabricius are destroyed, resulting in B-cell-dependent immunodeficiency. This causes increased susceptibility to diseases by otherwise harmless agents. The decisive role in the pathogenesis of IBD is played by the bursa, representing the target organ of the aetiological agent, infectious bursal disease virus (IBDV). By adaptation of IBDV to chicken embryo cells, we obtained several variants of a pathogenic wild type strain. These variants had altered abilities for replication in actively dividing B lymphocytes and, consequently, had altered pathogenic properties. An IBDV isolate from turkeys, non-pathogenic for chickens, was used to create reassortant virus strains. The virological and the biological characterization of these IBDV variants is reported.

Animals↗

PubMed2025

Novel Protein-Altering Variants in Cleft Genes Transmitted in Families With NSCL±P.

BACKGROUND: Pathogenic protein-altering variants play a role in the etiology of nonsyndromic cleft lip with or without palate (nsCL±P), one of the most common craniofacial anomalies. However, the genetic basis of many cases remains unclear, complicating risk prediction for affected families. PURPOSE: This study utilized whole-genome sequencing (WGS) of 150 case-families with nsCL±P from sub-Saharan Africa to identify pathogenic risk variants. STUDY DESIGN, SETTING, SAMPLE: This study utilized whole-genome sequencing (WGS) of 150 case-families with nsCL±P from sub-Saharan Africa to identify risk variants. PREDICTOR/EXPOSURE/INDEPENDENT VARIABLE: Genetic variants. MAIN OUTCOME VARIABLES: Nonsyndromic cleft lip with or without palate (nsCL±P). ANALYSES: Genomes were sequenced at a mean ×30 coverage, and variants were prioritized using CADD (≥20), REVEL (≥0.5), and ACMG/AMP clinical significance criteria. RESULTS: We identified pathogenic protein-altering variants in CHD7 (p.Arg1345His), LRP2 (p.Asp3245Asn), RYR1 (p.Arg2163Leu, p.Pro2903Thr), SHH (p.Met114Val), and WNT3 (p.Ser112Pro) highlighting the role of hedgehog signaling pathway (FDR=5.32e-12) in nsCL±P. These variants were inherited from unaffected parents suggesting an incomplete penetrance of the variant effect. Although mouse data showed that knockout of these genes produces cleft phenotypes, in vivo studies will help us better understand how the consequences of these variants differ from benign mutations. The presence of these protein-altering variants in unaffected parents-incomplete penetrance, provides additional evidence supporting the trait complexity. CONCLUSIONS AND RELEVANCE: This study identified rare, pathogenic protein-altering variants in genes involved in key developmental pathways in African families affected by nsCL±P. These findings highlight the critical role of the hedgehog signaling pathway and related networks in the etiology of nsCL±P. These findings underscore the importance of whole-genome sequencing in genetically diverse populations to uncover novel risk variants. These findings enhance our understanding of the genetic etiology of nsCL±P, particularly in under-represented African populations and support the multifactorial inheritance and the involvement of developmental pathways, such as hedgehog signaling in the etiology of clefting.

Humans↗

PubMed2025

DNA-binding affinity and specificity determine the phenotypic diversity in BCL11B-related disorders.

BCL11B is a Cys2-His2 zinc-finger (C2H2-ZnF) domain-containing, DNA-binding, transcription factor with established roles in the development of various organs and tissues, primarily the immune and nervous systems. BCL11B germline variants have been associated with a variety of developmental syndromes. However, genotype-phenotype correlations along with pathophysiologic mechanisms of selected variants mostly remain elusive. To dissect these, we performed genotype-phenotype correlations of 92 affected individuals harboring a pathogenic or likely pathogenic BCL11B variant, followed by immune phenotyping, analysis of chromatin immunoprecipitation DNA-sequencing data, dual-luciferase reporter assays, and molecular modeling. These integrative analyses enabled us to define three clinical subtypes of BCL11B-related disorders. It is likely that gene-disruptive BCL11B variants and missense variants affecting zinc-binding cysteine and histidine residues cause mild to moderate neurodevelopmental delay with increased propensity for behavioral and dental anomalies, allergies and asthma, and reduced type 2 innate lymphoid cells. Missense variants within C2H2-ZnF DNA-contacting α helices cause highly variable clinical presentations ranging from multisystem anomalies with demise in the first years of life to late-onset, hyperkinetic movement disorder with poor fine motor skills. Those not in direct DNA contact cause a milder phenotype through reduced, target-specific transcriptional activity. However, missense variants affecting C2H2-ZnFs, DNA binding, and "specificity residues" impair BCL11B transcriptional activity in a target-specific, dominant-negative manner along with aberrant regulation of alternative DNA targets, resulting in more severe and unpredictable clinical outcomes. Taken together, we suggest that the phenotypic severity and variability is largely dependent on the DNA-binding affinity and specificity of altered BCL11B proteins.

Adolescent↗

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↗

PubMed2006

HIV-1 fitness and disease progression: insights from the SIV-macaque model.

Within the initial weeks following transmission, HIV-1 becomes well established in the lymphatic tissue reservoir. Replication of the virus occurs throughout the course of infection despite the induction of a vigorous adaptive immune response by the host. The emergence of variants with particular characteristics correlates with increased viral burden and disease progression, indicating that the fitness of the infecting virus and selected variants plays a significant role in persistent viral replication and disease progression. This article reviews studies of HIV-1 variants and pathogenicity. It focuses mainly on experimental SIV infection of macaques as a model system to decipher the significance of viral variants for infection, persistence, and disease because it is difficult to systematically examine transmission and pathogenesis of HIV-1 in humans.

Animals↗

PubMed2000

Molecular characterization of guinea pig-adapted variants of Ebola virus.

Serial passage of initially nonlethal Ebola virus (EBOV) in outbred guinea pigs resulted in the selection of variants with high pathogenicity. Nucleotide sequence analysis of the complete genome of the guinea pig-adapted variant 8mc revealed that it differed from wild-type virus by eight mutations. No mutations were identified in nontranscribed regions, including leader, trailer, and intragenic sequences. Among noncoding regions the only base change was found in the VP30 gene. Two silent base changes were found in the open reading frame (ORF) encoding NP protein. Nucleotide changes resulting in single-amino-acid exchanges were identified in both NP and L genes. Three other mutations found in VP24 caused amino acid substitutions, which are responsible for larger structural changes of this protein, as indicated by an alteration in electrophoretic mobility. A highly pathogenic EBOV variant K5 from another passaging series showed an amino acid substitution at nearly the same location in the VP24 gene, suggesting the importance of this protein in the adaptation process. In addition, sequence variability of the GP gene was found when plaque-purified clones of EBOV-8mc were analyzed. Three of five viral clones showed insertion of one uridine residue at the GP gene-editing site, which led to a significant change in the expression of virus glycoproteins. This observation suggests that the editing site is a hot spot for insertion and deletion of nucleotides, not only at the level of transcription but also of genome replication. Irrespective of the number of uridine residues at the editing site, all plaque-purified clones of EBOV variant 8mc resembled each other in their pathogenicity for guinea pigs, indicating either the absence or only supportive role of mutations in the GP gene on the adaptation process.

Amino Acid Substitution↗

PubMed2022

Mortality Among Patients With Early-Onset Atrial Fibrillation and Rare Variants in Cardiomyopathy and Arrhythmia Genes.

IMPORTANCE: Patients with early-onset atrial fibrillation (AF) are enriched for rare variants in cardiomyopathy and arrhythmia genes. The clinical significance of these rare variants in patients with early-onset AF is unknown. OBJECTIVE: To assess the association between rare variants in cardiomyopathy and arrhythmia genes detected in patients with early-onset AF and time to death. DESIGN, SETTING, AND PARTICIPANTS: This prospective cohort study included participants with AF diagnosed before 66 years of age who underwent whole-genome sequencing through the National Heart, Lung and Blood Institute's Trans-Omics for Precision Medicine program. Participants were enrolled from November 23, 1999, to June 2, 2015. Data were analyzed from February 26 to September 19, 2021. EXPOSURES: Rare variants identified in a panel of 145 genes that are included in cardiomyopathy and arrhythmia panels used by commercial clinical genetic testing laboratories. MAIN OUTCOMES AND MEASURES: The primary study outcome was time to death and was adjudicated from medical records and the National Death Index. Multivariable Cox proportional hazards regression was used to evaluate the association of disease-associated variants with risk of death after adjustment for age at AF diagnosis, sex, race, body mass index, left ventricular ejection fraction, and an interaction term of age at AF diagnosis and disease-associated variant status. RESULTS: Among 1293 participants (934 [72%] male; median age at enrollment, 56.0 years; IQR, 48.0-61.0 years), disease-associated (pathogenic or likely pathogenic) rare variants were found in 131 (10%). During a median follow-up of 9.9 years (IQR, 6.9-13.2 years), 219 participants (17%) died. In univariable analysis, disease-associated variants were associated with an increased risk of mortality (hazard ratio, [HR], 1.5; 95% CI, 1.0-2.1; P = .05); the association remained significant in multivariable modeling when adjusted for age at AF diagnosis, sex, race, body mass index, left ventricular ejection fraction, and an interaction term between disease-associated variant status and age at AF diagnosis. The interaction demonstrated that disease-associated variants were associated with a significantly higher risk of mortality compared with no disease-associated variant when AF was diagnosed at a younger age (P = .008 for interaction). Higher body mass index (per IQR: HR, 1.4; 95% CI, 1.2-1.6; P < .001) and lower left ventricular ejection fraction (per IQR: HR, 0.8; 95% CI, 0.7-0.8; P < .001) were associated with higher mortality risk. There were 73 cardiomyopathy-related deaths, 40 sudden deaths, and 10 stroke-related deaths. Mortality among patients with the most prevalent genes with disease-associated variants was 26% (10 of 38 patients) for TTN, 33% (6 of 18) for MYH7, 22% (2 of 9) for LMNA, 0% (0 of 10) for MYH6, and 0% (0 of 8) for KCNQ1. CONCLUSIONS AND RELEVANCE: The findings suggest that rare variants in cardiomyopathy and arrhythmia genes may be associated with increased risk of mortality among patients with early-onset AF, especially those diagnosed at a younger age. Genetic testing may provide important prognostic information for patients with early-onset AF.

Atrial Fibrillation↗

PubMed2026

Next-generation newborn screening: feasibility of combined genetic and biochemical testing for 95 treatable inherited metabolic disorders.

INTRODUCTION: Next-generation sequencing (NGS) is gaining attention in newborn screening (NBS) for its ability to detect treatable genetic disorders, especially those without a biochemical footprint. However, NGS-NBS requires interpreting variants without phenotype information or family trio analysis. Biochemical tests, preferably in dried blood spots (DBS), are therefore useful to confirm the pathogenicity of variants identified by NGS-NBS and increase its specificity and sensitivity. OBJECTIVES: We aimed to explore the potential of combined genetic-biochemical testing for 95 treatable Inherited Metabolic Disorders (IMD) considered eligible for NGS-NBS (100 genes) previously identified by our research group. METHODS: We reviewed the Collaborative Laboratory Integrated Reports (CLIR) and carried out systematic literature reviews in PubMed and Embase to identify biochemical tests for 95 IMD. Biochemical tests conducted on DBS were differentiated from tests that require referral. RESULTS: We identified DBS-biochemical tests for 72 of the 95 IMD (77/100 genes). DBS-based biochemical tests for 55 IMD (60 genes) are already implemented in NBS. For the other 23 IMD, biochemical tests in non-DBS specimens are reported, although some are less sensitive when measured at neonatal age in presymptomatic infants. CONCLUSION: We present a comprehensive overview of current biochemical tests for 95 IMD. These tests can be used to confirm inconclusive NGS-NBS results, and combined genetic-biochemical testing is expected to improve both the negative and positive predictive values of NBS programs.

Humans↗

PubMed1979

Selection of small-colony variants of Enterobacteriaceae by in vitro exposure to aminoglycosides: pathogenicity for experimental animals.

Small-colony variants of gram-negative genera of Enterobacteriaceae were selected by in vitro exposure to gentamicin. These variants were shown to have decreased susceptibility in vitro to aminoglycosides. They were lethal for mice following intraperitoneal injection, with the LD50 (50% lethal dose) being the same as, or slightly less than, that for the parent organism. Variants of strain no. 2401 of Proteus mirabilis caused urinary tract infection in mice after implantation into their bladders. Although the variants grew somewhat less rapidly than did parent organisms, both parent and variant colonies alkalinized urine at the same rate. Electron microscopic study showed no differences between colonies of parents and variants. These studies indicated that small-colony variants of Enterobacteriaceae are pathogenic for experimental animals. Further, they may cause disease in humans and should not necessarily be regarded as only laboratory curiosities.

Aminoglycosides↗

PubMed2026

Bayesian Integration of Tumor Mutational Signatures and Somatic Features Refines Pathogenicity Assessment of Germline Mismatch Repair Variants.

Variants of uncertain significance (VUS) in mismatch repair (MMR) genes represent a persistent bottleneck in germline interpretation for Lynch syndrome, creating a critical opportunity to leverage tumor biology to refine pathogenicity assessment. Although tumor features such as microsatellite instability (MSI) and immunohistochemistry (IHC) are routinely evaluated, they are typically interpreted separately from germline classification, and their quantitative contribution within ACMG/AMP frameworks remains poorly defined. We therefore analyzed paired germline and tumor sequencing data from 1110 tumors across 1073 patients with colorectal or endometrial cancer to determine whether mismatch repair-deficient (MMR-d) mutational signatures can be quantitatively integrated into Bayesian germline variant interpretation. Using COSMIC single-base substitution signatures, tumors were classified as MMR-d or MMR proficient, and an empirically derived likelihood ratio (LR) quantified the association between MMR-d signatures and pathogenic germline MMR variants. The presence of an MMR-d signature increased the likelihood of an underlying pathogenic germline MMR variant approximately eightfold (LR ≈ 8; log10 LR ≈ 0.90), whereas its absence provided moderate-to-strong benign evidence (LR ≈ 0.156; log10 LR ≈ -0.81). Applying this integrative framework to 45 germline MMR VUS, joint modeling of tumor mutational signatures with additional somatic and variant-level evidence resulted in clinically significant reclassification of 38 (84.4%) variants, including three reclassified as pathogenic or likely pathogenic and 35 as likely benign. A total of 16 downgraded variants were independently downgraded by Invitae. These findings demonstrate that tumor mutational signatures can be formally incorporated into Bayesian germline interpretation, transforming tumor data into quantitative pathogenicity evidence and offering a principled strategy to reduce VUS burden in hereditary cancer genetics.

Humans↗