The role of comprehensive analysis with circulating tumor DNA in advanced non-small cell lung cancer patients considered for osimertinib treatment

Background

EGFR mutations are good predictive markers of efficacy of EGFR tyrosine kinase inhibitors (EGFR‐TKI), but whether comprehensive genomic analysis beyond EGFR itself with circulating tumor DNA (ctDNA) adds further predictive or prognostic value has not been clarified.

Methods

Patients with NSCLC who progressed after treatment with EGFR‐TKI, and with EGFR T790 M detected by an approved companion diagnostic test (cobas^®), were treated with osimertinib. Plasma samples were collected before and after treatment. Retrospective comprehensive next‐generation sequencing (NGS) of ctDNA was performed with Guardant360^®. Correlation between relevant mutations in ctDNA prior to treatment and clinical outcomes, as well as mechanisms of acquired resistance, were analyzed.

Results

Among 147 patients tested, 57 patients received osimertinib, with an overall response rate (ORR) of 58%. NGS was successful in 54 of 55 available banked plasma samples; EGFR driver mutations were detected in 43 (80%) and T790 M in 32 (59%). The ORR differed significantly depending on the ratio (T790 M allele fraction [AF])/(sum of variant AF) in ctDNA (p = 0.044). The total number of alterations detected in plasma by NGS was higher in early resistance patients (p = 0.025). T790 M was lost in 32% of patients (6 out of 19) after acquired resistance to osimertinib. One patient with RB1 deletion and copy number gains of EGFR, PIK3CA, and MYC in addition to T790 M, showed rapid progression due to suspected small cell transformation.

Conclusions

NGS of ctDNA could be a promising method for predicting osimertinib efficacy in patients with advanced NSCLC harboring EGFR T790 M.

Novel Compound Heterozygous Pathogenic Variants in SUOX Cause Isolated Sulfite Oxidase Deficiency in a Chinese Han Family

Aim

To explore the clinical imaging, laboratory and genetic characteristics of a newborn boy with isolated sulfite oxidase deficiency (ISOD) in a Chinese mainland cohort.

Methods

Homocysteine and uric acid in plasma and cysteine and total homocysteine in the blood spot were assessed in a Chinese newborn patient with progressive encephalopathy, tonic seizures, abnormal muscle tone, and feeding difficulties. Whole exome sequencing and Sanger sequencing facilitated an accurate diagnosis. The pathogenicity predictions and conservation analysis of the identified mutations were conducted by bioinformatics tools.

Results

Low total homocysteine was detected in the blood spot, while homocysteine and uric acid levels were normal in the plasma. S-sulfocysteine was abnormally elevated in urine. A follow-up examination revealed several progressive neuropathological findings. Also, intermittent convulsions and axial dystonia were observed. However, the coordination of sucking and swallowing was slightly improved. A novel paternal nonsense variant c.475G > T (p.Glu159^∗) and a novel maternal missense variant c.1201A > G (p.Lys401Glu) in SUOX were identified in this case by co-segregation verification.

Conclusion

This is the second report of early-onset ISOD case in a non-consanguineous Chinese mainland family. Combined with the clinical characteristics and biochemical indexes, we speculated that these two novel pathogenic variants of the SUOX gene underlie the cause of the disease in this patient. Next-generation sequencing (NGS) and Sanger sequencing provided reliable basis for clinical and prenatal diagnoses of this family, it also enriched the mutation spectrum of the SUOX gene.

Evaluation of the diagnostic performance of nine commercial RT-PCR kits for the detection of SARS-CoV-2 in Colombia

The ongoing severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic has led to the design and development of multiple reverse‐transcription polymerase chain reaction kits aimed to facilitate the rapid scale‐up of molecular testing for massive screening. We evaluated the diagnostic performance of nine commercial kits, which showed optimal performance and high discriminatory power. However, we observed differences in terms of sensitivity, specificity, and E gene Ct Values and discuss these results in light of the influence of SARS‐CoV‐2 genetic variability and its potential impact in current molecular diagnostic assays.

Congenital erythrocytosis

Erythrocytosis, or increased red cell mass, may be labeled as primary or secondary, depending on whether the molecular defect is intrinsic to the red blood cells/their precursors or extrinsic to them, the latter being typically associated with elevated erythropoietin (EPO) levels. Inherited/congenital erythrocytosis (CE) of both primary and secondary types is increasingly recognized as the cause in many patients in whom acquired, especially neoplastic causes have been excluded. During the past two decades, the underlying molecular mechanisms of CE are increasingly getting unraveled. Gain-in-function mutations in the erythropoietin receptor gene were among the first to be characterized in a disorder termed primary familial and congenital polycythemia. Another set of mutations affect the components of the oxygen-sensing pathway. Under normoxic conditions, the hypoxia-inducible factor (HIF), upon hydroxylation by the prolyl-4-hydroxylase domain protein 2 (PHD2) enzyme, is degraded by the von Hippel-Lindau protein. In hypoxic conditions, failure of prolyl hydroxylation leads to stabilization of HIF and activation of the EPO gene. CE has been found to be caused by loss-of-function mutations in VHL and PHD2/EGLN1 as well as gain-of-function mutations in HIF-2α (EPAS1), all resulting in constitutive activation of EPO signaling. Apart from these, globin gene mutations leading to formation of high oxygen affinity hemoglobins also cause CE. Rarely, bisphosphoglycerate mutate mutations, affecting the 2,3-bisphosphoglycerate levels, can increase the oxygen affinity of hemoglobin and cause CE. This narrative review examines the current mutational spectrum of CE and the distinctive pathogenetic mechanisms that give rise to this increasingly recognized condition in various parts of the world.

Spectrum of DICER1 Germline Pathogenic Variants in Ovarian Sertoli-Leydig Cell Tumor

Sertoli–Leydig Cell Tumors (SLCTs) are rare ovarian sex cord-stromal neoplasms, which predominantly affect adolescents and young female adults. The SLCTs clinical diagnosis and treatment remains challenging due to the rarity and the varied presentation. A large majority of SLCTs are unilateral, but also bilateral neoplasms have been reported, sometimes in the context of DICER1 syndrome. In fact, the most significant discovery regarding the molecular genetics basis of SLCTs was the finding of somatic and germline pathogenic variants in the DICER1 gene. The DICER1 protein is a key component of the micro-RNA processing pathway. Germline DICER1 pathogenic variants are typically inherited in an autosomal dominant pattern and are most often loss-of-function variants dispersed along the length of the gene. Contrarily, DICER1-related tumors harbor a characteristic missense “RNase IIIb hotspot” mutation occurring in trans, or, less frequently, loss of heterozygosity (LOH) event involving the wild-type allele. While DICER1 mutations have been identified in approximately 60% of SLCTs, especially in the moderately or poorly differentiated types, there are only a few case reports of ovarian SLCT with underlying germline DICER1 mutations. In this review, we focus on the molecular genetic features of SLCT, performing an extensive survey of all germline pathogenic variants modifying the whole sequence of the DICER1 gene. We point out that DICER1 genetic testing, coupled with an accurate variants classification and timely counseling, is of crucial importance in the clinical management of ovarian SLCT-affected patients.

Deciphering the mutational signature of congenital limb malformations

Congenital limb malformations (CLMs) affect 1 in 500 live births. However, the value of exome sequencing (ES) for CLM is lacking. The purpose of this study was to decipher the mutational signature of CLM on an exome level. We enrolled a cohort of 66 unrelated probands (including 47 families) with CLM requiring surgical correction. ES was performed for all patients and available parental samples. A definite molecular diagnosis was achieved in 21 out of 66 (32%) patients. We identified 19 pathogenic or likely pathogenic single-nucleotide variants and three copy number variants, of which 11 variants were novel. We identified four variants of uncertain significance. Additionally, we identified RPL9 and UBA2 as novel candidate genes for CLM. By comparing the detailed phenotypic features, we expand the phenotypic spectrum of diastrophic dysplasia and chromosome 6q terminal deletion syndrome. We also found that the diagnostic rate was significantly higher in patients with a family history of CLM (p = 0.012) or more than one limb affected (p = 0.034). Our study expands our understanding of the mutational and phenotypic spectrum of CLM and provides novel insights into the genetic basis of these syndromes.

Evaluation of the Performance of the Loopamp Trypanosoma cruzi Detection Kit for the Diagnosis of Chagas Disease in an Area Where It Is Not Endemic, Spain

In Spain, PCR is the tool of choice for the diagnosis of congenital Chagas disease (CD) and serology for diagnosing chronic CD. A loop-mediated isothermal amplification test for Trypanosoma cruzi DNA detection showed good analytical performance and ease of use.

In Spain, PCR is the tool of choice for the diagnosis of congenital Chagas disease (CD) and serology for diagnosing chronic CD. A loop-mediated isothermal amplification test for Trypanosoma cruzi DNA detection showed good analytical performance and ease of use. We aimed to evaluate the performance of the Loopamp Trypanosoma cruzi detection kit (Eiken Chemical Co. Ltd., Japan) (Tcruzi-LAMP) for congenital and chronic CD diagnosis using well-characterized samples. We included samples from 39 congenital and 174 chronic CD cases and from 48 uninfected children born to infected mothers and 34 nonchagasic individuals. The sensitivity, specificity, and accuracy of Tcruzi-LAMP were estimated using standard case definitions for congenital CD (positive result by parasitological or PCR tests or serology after 9 months of age) and chronic CD (positive serology by at least two tests). The Tcruzi-LAMP results were read by visual examination and a real-time fluorimeter. For congenital CD, Tcruzi-LAMP sensitivity was 97% for both types of reading; specificity was 92% by visual examination and 94% by fluorimeter. For chronic CD, sensitivity was 47% and specificity 100%. The accuracy in congenital CD was >94% versus 56% in chronic CD. The agreement of Tcruzi-LAMP with PCR tests was better in congenital CD (kappa, 0.86 to 0.91) than in chronic CD (kappa, 0.67 to 0.83). The Loopamp Trypanosoma cruzi detection kit showed good performance for the diagnosis of congenital CD. Tcruzi-LAMP, like PCR, can be useful for the screening and early diagnosis of congenital infection.

Molecular epidemiological insights into Trypanosoma vivax in Argentina: From the endemic Gran Chaco to outbreaks in the Pampas

Argentina is a home to millions of beef and dairy cattle and is one of the world's major exporters of meat. In the present study, Trypanosoma vivax was prevalent (2016-2018) in two major livestock farming regions, the Gran Chaco and the Pampas. In the Gran Chaco, 29% and 51% of animals (n = 72, taurine x zebuine crossbreed) were, respectively, positive by TviCATL-PCR and the more sensitive fluorescent fragment length barcoding (FFLB) method. While 18.4/38.8% of breeding cows (n = 49) tested positive by PCR/FFLB, infection increased to 52.2/78.3% in an outbreak of acute infection in steers (n = 23, taurine breed) brought from a non-endemic area. In the Pampas, overall infection rates in dairy cows (n = 54, taurine breed) were comparable (p > .01) between PCR (66.7%) and FFLB (62.9%) and showed a remarkable increase (PCR / FFLB) from 48.3/44.8% in 2017 to 88/84% in 2018. Infected dairy cattle exhibited anaemia, fever, anorexia, enlarged lymph nodes, emaciation and neurological signs. In contrast, beef cows (taurine x zebuine crossbreed) from the Pampas (n = 30) were asymptomatic despite exhibiting 16.7% (PCR) and 53.3% (FFLB) infection rates. Microsatellite genotyping revealed a remarkable microheterogeneity, seven genotypes in the Gran Chaco, nine in the Pampas and five shared between both regions, consistent with regular movement of T. vivax infected livestock. Data gathered in our study support the Gran Chaco being an endemic area for T. vivax, whereas the Pampas emerged as an outbreak area of acute infection in dairy cattle with critical negative impact in milk production. To the best of our knowledge, this is the first molecular study of T. vivax in Argentina, and results indicated the need for preventive measures to control T. vivax spread from the Gran Chaco to vast livestock farming areas across Argentina.

Personalized medicine for allergy treatment: Allergen immunotherapy still a unique and unmatched model

The introduction of personalized medicine (PM) has been a milestone in the history of medical therapy, because it has revolutionized the previous approach of treating the disease with that of treating the patient. It is known today that diseases can occur in different genetic variants, making specific treatments of proven efficacy necessary for a given endotype. Allergic diseases are particularly suitable for PM, because they meet the therapeutic success requirements, including a known molecular mechanism of the disease, a diagnostic tool for such disease, and a treatment blocking the mechanism. The stakes of PM in allergic patients are molecular diagnostics, to detect specific IgE to single-allergen molecules and to distinguish the causative molecules from those merely cross-reactive, pursuit of patient's treatable traits addressing genetic, phenotypic, and psychosocial features, and omics, such as proteomics, epi-genomics, metabolomics, and breathomics, to forecast patient's responsiveness to therapies, to detect biomarker and mediators, and to verify the disease control. This new approach has already improved the precision of allergy diagnosis and is likely to significantly increase, through the higher performance achieved with the personalized treatment, the effectiveness of allergen immunotherapy by enhancing its already known and unique characteristics of treatment that acts on the causes.

The thyroid risk score (TRS) for nodules with indeterminate cytology

Cytology is the gold standard method for the differential diagnosis of thyroid nodules, though 25-30% of them are classified as indeterminate. We aimed to set up a 'thyroid risk score' (TRS) to increase the diagnostic accuracy in these cases. We prospectively tested 135 indeterminate thyroid nodules. The pre-surgical TRS derived from the sum of the scores assigned at cytology, EU-TIRADS classification, nodule measurement, and molecular characterization, which was done by our PTC-MA assay, a customized array able to cost-effectively evaluate 24 different genetic alterations including point mutations and gene fusions. The risk of malignancy (ROM) increased paralleling the score: in the category >4 and ≤ 6 (low suspicion), >6 ≤ 8 (intermediate suspicion), and >8 (high suspicion); ROM was 10, 47 and 100%, respectively. ROC curves selected the score >6.5 as the best threshold to differentiate between malignant and benign nodules (P < 0.001). The TRS > 6.5 had a better performance than the single parameters evaluated separately, with an accuracy of 77 and 82% upon inclusion of noninvasive follicular thyroid neoplasm with papillary-like nuclear features among malignant or benign cases, respectively. In conclusion, for the first time, we generated a score combining a cost-effective molecular assay with already validated tools, harboring different specificities and sensitivities, for the differential diagnosis of indeterminate nodules. The combination of different parameters reduced the number of false negatives inherent to each classification system. The TRS > 6.5 was highly suggestive for malignancy and retained a high accuracy in the identification of patients to be submitted to surgery.

Molecular Characterization of an Emerging Root-Knot Nematode Meloidogyne enterolobii in North Carolina, USA

An emerging threat to agriculture, Meloidogyne enterolobii Yang & Eisenback, 1983, is a tropical species and considered to be the most damaging root-knot nematode (RKN) in the world because of its wide host range, aggressiveness, and ability to overcome resistance to RKN in many crops. It was first detected in the United States on ornamental plants in Florida in 2001 but has since been identified in North Carolina, South Carolina, and Louisiana. Several thousand RKN populations were collected from North Carolina field crops, ornamental plants, and turfgrasses for species identification in the Nematode Assay Laboratory in the North Carolina Department of Agriculture & Consumer Services. From 2006 to 2019, root systems showing galling symptoms were dissected under the microscope, and females were obtained for DNA analysis. When only soil samples were submitted, the second-stage juveniles or males were used instead. Molecular characterization was performed via polymerase chain reaction with species-specific primers and DNA sequencing on the ribosomal DNA 18S-ITS1-5.8S and 28S D2/D3 and mitochondrial DNA CoxII-16S. One hundred thirty-five representative RKN populations from North Carolina were characterized and identified as M. enterolobii. Six populations from China where the species was originally described were included in this study for identity confirmation and comparison. As of December 2019, M. enterolobii has been confirmed from a limited number of fields in 11 North Carolina counties: Columbus, Craven, Greene, Harnett, Johnston, Lenoir, Nash, Pitt, Sampson, Wayne, and Wilson. Currently, M. enterolobii is the most important emerging RKN species in the United States and causes severe damage to agronomic and horticultural crops, especially sweetpotato in North Carolina.

Setting up a molecular diagnostic laboratory for SARS-CoV-2 testing: Experience of a single centre in a resource-constrained setting

Background

Molecular detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is at the forefront of the global response to the coronavirus disease 2019 (COVID-19) pandemic. However, molecular diagnostic capabilities are poorly developed in many African countries. Efforts by the Nigeria Centre for Disease Control and other public health agencies to scale up facilities for molecular testing across the continent are well documented, but there are few accounts from the laboratories at the frontline.

Intervention

As part of an institutional response to the COVID-19 pandemic, the University of Benin Teaching Hospital, Benin City, Nigeria, signed a memorandum of understanding with a World Bank-supported institution to obtain a non-proprietary testing platform, renovated an existing molecular virology laboratory and validated the test process to make SARS-CoV-2 testing readily available for decision-making by frontline health workers. These efforts resulted in the University of Benin Teaching Hospital’s inclusion in the Nigeria Centre for Disease Control COVID-19 molecular laboratory network. The laboratory achieved a turnover of 12 123 tests within 7 months of operation. Challenges faced and dealt with include incompatible equipment, limited skilled manpower, unstable (unreliable) electric power supply, disrupted procurement and supply chain, and significant overhead costs.

Lessons learnt

Molecular diagnostic capability is essential in laboratory preparedness for pandemic response and can be achieved by establishing collaborative networks in low-resource settings.

Recommendations

Molecular diagnostic capabilities attained during the COVID-19 pandemic should be maintained by governmental support of the local biotechnology sector, collaboration with partners and stakeholders and the expansion of diagnostics to include other diseases of public health importance.

Diagnostic profile of the AmplideX Fragile X Dx and Carrier Screen Kit for diagnosis and screening of fragile X syndrome and other FMR1-related disorders

Introduction: In 2009, a novel, CGG repeat primed FMR1 PCR assay was designed with primers flanking the triplet repeat region, as well as a third chimeric primer complementary to the (CGG)n repeat, that was capable of amplifying alleles throughout the repeat range. This assay for the first time allowed consistent detection of large full mutation alleles with PCR, resolution of heterozygosity in females and mapping of AGG interspersions.Areas Covered: The AmplideX Fragile X Dx and Carrier Screen Kit (Asuragen, Inc.) represents a refined assay that underwent validation with sensitivity analyses for FDA approval. Single-site precision, analytical sensitivity and specificity, limit of detection and diagnostic performance were assessed in comparison to reference methods at three independent sites. Single-site precision across all genotype categories showed 100% agreement at 20 ng input across multiple operators, days, instruments and kit lots. Compared to Southern Blot analysis, the overall percent agreement was over 98% for all expanded alleles.Expert Opinion: Limitations include no methylation assessment and hard to see full mutation peaks in some mosaic samples, but overall the assay is considered a highly accurate and time-efficient assay for FMR1 allele size determination.

Comparison Between a Standard and SalivaDirect RNA Extraction Protocol for Molecular Diagnosis of SARS-CoV-2 Using Nasopharyngeal Swab and Saliva Clinical Samples

During the COVID-19 pandemic, a certified laboratory of Tamaulipas, Mexico has processed over 100,000 samples of COVID-19 suspected patients, working a minimum of 100 tests daily. Thus, it would be beneficial for such certified laboratories nationwide to reduce the time and cost involved in performing the diagnosis of COVID-19, from sample collection, transportation to local lab, processing of samples, and data acquisition. Here, 30 nasopharyngeal swab and saliva samples from the same COVID-19 individuals were assessed by a standard nucleic acid extraction protocol, including protein lysis with proteinase K followed by binding to column, washing, and elution, and by the SalivaDirect protocol based on protein lysis, skipping the other steps to reduce processing time and costs. The genomic RNA was amplified using a SARS-CoV-2 Real-Time PCR kit. A variation (P > 0.05) in the 95% CIs = 72.6%–96.7% was noted by using the SalivaDirect protocol and saliva samples (sensitivity of 88.2%) in comparison to those of standard protocol with oropharyngeal swab samples (95% CIs = 97.5%–100%; sensitivity of 100%) as reported elsewhere. However, when using nasopharyngeal swab samples in the SalivaDirect protocol (sensitivity of 93.6%; 95% CIs = 79.2%–99.2%), it was in concordance (P < 0.05) with those of the standard one. The logical explanation to this was that two samples with Ct values of 38, and 40 cycles for gene E produced two false negatives in the SalivaDirect protocol in relation to the standard one; thus, there was a reduction of the sensitivity of 6.4% in the overall assay performance.

First Molecular Confirmation of Equine Ocular Setaria digitata in China

A 5-year-old Mongolian mare (Equus caballus Linnaeus, 1758) was observed to have corneal opacity and excessive ocular discharge. An ophthalmic examination revealed a moving thread-like cylindrical worm in the anterior chamber of the right eye. The parasite was successfully removed surgically. The worm was observed under light microscopy and confirmed as Setaria digitata by 12S rRNA gene amplification and sequencing. Phylogenetic analysis demonstrated similarity with Setaria digitata in the National Center for Biotechnology Information (NCBI) GenBank database isolated from other Asian countries. This report is the first confirmed case of equine ocular setariasis by molecular diagnosis in China, which may indicate its presence in livestock and promote research on its epidemiology.

Use of Next-Generation Sequencing for the Molecular Diagnosis of 1,102 Patients With a Autosomal Optic Neuropathy

Advances in next-generation sequencing (NGS) facilitate the diagnosis of genetic disorders. To evaluate its use for the molecular diagnosis of inherited optic neuropathy (ION), a blinding disease caused by the degeneration of retinal ganglion cells, we performed genetic analysis using targeted NGS of 22 already known and candidate genes in a cohort of 1,102 affected individuals. The panel design, library preparation, and sequencing reactions were performed using the Ion AmpliSeq technology. Pathogenic variants were detected in 16 genes in 245 patients (22%), including 186 (17%) and 59 (5%) dominant and recessive cases, respectively. Results confirmed that OPA1 variants are responsible for the majority of dominant IONs, whereas ACO2 and WFS1 variants are also frequently involved in both dominant and recessive forms of ION. All pathogenic variants were found in genes encoding proteins involved in the mitochondrial function, highlighting the importance of mitochondria in the survival of retinal ganglion cells.

Laboratory-based diagnosis of scabies: a review of the current status

Scabies is a neglected tropical disease (NTD) of the skin that is caused by the mite Sarcoptes scabiei. It is considered to be an important public health problem in many regions. The disease is at its most prevalent in low-resource countries where there are overcrowded living conditions coupled with poor hygiene. In some regions, mass drug administration using ivermectin is a key population-based approach to the control of scabies. Before starting a patient on specific treatment, confirming the diagnosis by accurate and rapid identification of the organism is critical. Different laboratory-based techniques for scabies have been developed in the last few decades. These include direct microscopy and histopathology. More recently, serological testing, dermoscopy and different molecular techniques have been developed as diagnostic methods for scabies. To date, none of these, apart from microscopy and dermoscopy, has been translated into routine clinical laboratory practice. A simple point-of-care or laboratory test would provide a rapid and confirmed diagnosis and early institution of effective treatment. In this review we present an update on the laboratory techniques currently in use for the identification of scabies.

En route to personalized medicine: uncovering distinct IgE reactivity pattern to house dust mite components in Brazilian and Austrian allergic patients

AIM

Molecular sensitization profile analyses of allergic individuals to the house dust mites (HDM) Blomia tropicalis and Dermatophagoides pteronyssinus from Brazil and Austria, in the attempt to comprehend the individual contribution of the molecular components in the diagnosis of HDM allergy.

METHODOLOGY

These analyses were made using a new in vitro multiplex allergen assay which allows simultaneous measurement of specific IgE against the whole allergen extract as well its components.

RESULTS AND CONCLUSION

The data showed that in Brazil the inclusion of the molecular components Blo t 5 and/or Blo t 21 major allergens and Blo t 2 can increase the sensitivity and specificity of the assay for the diagnosis of allergy to B. tropicalis, using matrix-based methodologies. Also we highlighted, for the first time, the importance of Blo t 2 analysis for a sensitive diagnosis, since some individuals were sensitized only to this molecular component. Regarding the sensitization profile of individuals sensitized to D. pteronyssinus, we point out the importance of analyzing the molecular components Der p23 and Der p 7, in addition to Der p 1 and Der p 2 for an accurate diagnosis based on matrices.

Symptom patterns and comparison of diagnostic methods in ragweed pollen allergy

The aim of the present study was to determine the pattern of symptoms of ragweed pollen-induced allergic disease in sensitized patients from Romania and to compare the molecular diagnosis of allergy with the skin prick test, in order to better characterize allergic patients and to guide therapy. A total of 97 subjects, including patients with ragweed pollen-induced allergic rhinoconjunctivitis with/without asthma, as well as healthy controls, were recruited prospectively in one ragweed pollen season, submitted to allergy questionnaires, skin prick tests and multiplex specific IgE (immunoglobulin E) measurement by ImmunoCAP ISAC (ImmunoCAP Immuno-Solid phase Allergy Chip) assay. A total of 83 patients were sensitized to ragweed pollen. Most patients (73%) were diagnosed with moderate-severe intermittent allergic rhinoconjunctivitis and 25% of the patients also had allergic asthma. The most common symptoms were watery rhinorrhea (91.57%), nasal obstruction (86.75%), and sneezing (85.54%). Most patients were polysensitized (62.65%), especially to other pollens, house dust mites and animal danders. Only 90% of the patients with positive skin prick test to ragweed pollen extract also had increased specific serum IgE to Amb a 1. Current options for specific molecular diagnosis of ragweed allergy are limited, as they only contain one or few of the sensitizing allergens present in ragweed pollen. An improved component-resolved diagnosis, using several ragweed pollen allergens, is required for better patient characterization and subsequent selection of an appropriate allergen immunotherapy product, thereby enabling a more personalized approach to the management of the ragweed-allergic patient.

Application of a Genus-Specific LAMP Assay for Schistosome Species to Detect Schistosoma haematobium x Schistosoma bovis Hybrids

Schistosomiasis is a disease of great medical and veterinary importance in tropical and subtropical regions caused by different species of parasitic flatworms of the genus Schistosoma. The emergence of natural hybrids of schistosomes indicate the risk of possible infection to humans and their zoonotic potential, specifically for Schistosoma haematobium and S. bovis. Hybrid schistosomes have the potential to replace existing species, generate new resistances, pathologies and extending host ranges. Hybrids may also confuse the serological, molecular and parasitological diagnosis. Currently, LAMP technology based on detection of nucleic acids is used for detection of many agents, including schistosomes. Here, we evaluate our previously developed species-specific LAMP assays for S. haematobium, S. mansoni, S. bovis and also the genus-specific LAMP for the simultaneous detection of several Schistosoma species against both DNA from pure and, for the first time, S. haematobium x S. bovis hybrids. Proper operation was evaluated with DNA from hybrid schistosomes and with human urine samples artificially contaminated with parasites' DNA. LAMP was performed with and without prior DNA extraction. The genus-specific LAMP properly amplified pure Schistosoma species and different S. haematobium-S. bovis hybrids with different sensitivity. The Schistosoma spp.-LAMP method is potentially adaptable for field diagnosis and disease surveillance in schistosomiasis endemic areas where human infections by schistosome hybrids are increasingly common.

Zoonotic Giardia duodenalis sub-assemblage BIV in wild raccoons (Procyon lotor) from Germany and Luxembourg

Giardia duodenalis is a cosmopolitan flagellate that causes giardiasis, one of the most significant gastrointestinal diseases in humans. This parasite can be a serious threat to public health because it can cause waterborne outbreaks as well as sporadic infections in humans. Invasive raccoons (Procyon lotor) may play a role in disseminating Giardia into the environment and transmitting it to humans and domestic animals because they live in high densities and deposit their faces in latrines near areas used by humans. While Giardia infections have been reported from raccoons in North America, it is unknown whether they carry G. duodenalis with zoonotic assemblage A and B, which have the potential to cause illness in humans. We collected faecal samples from 66 legally harvested raccoons in Germany and Luxembourg and examined for Giardia using molecular techniques. Using a quantitative PCR based on primers specific to Giardia genetic assemblages A and B, we detected the presence of zoonotic assemblage B in 27% (95% CI, 17.0-39.6) of all examined faecal samples from raccoons, including animals sampled in buildings. We did not detect genetic assemblage A in any of the samples. Sequences obtained from the glutamate dehydrogenase and beta-giardin gene fragments from a selection of three of the positive samples showed that raccoons carried a zoonotic G. duodenalis genotype belonging to sub-assemblage BIV, which is commonly found in humans and animals worldwide. Our results suggest that free-ranging raccoons have the potential to play an increasingly important role in the epidemiology of Giardia and pose a threat to public health in Europe and other regions where this species is common and lives in close association with humans.

A single NGS-based assay covering the entire genomic sequence of the DMD gene facilitates diagnostic and newborn screening confirmatory testing

Molecular diagnosis for Duchenne and Becker muscular dystrophies (DMD/BMD) involves a two-tiered approach for detection of deletions/duplications using MLPA or array CGH, followed by sequencing of coding and flanking intronic regions to detect sequence variants, which is time-consuming and expensive. We have developed a comprehensive next-generation sequencing (NGS)-based single-step assay to sequence the entire 2.2 Mb of the DMD gene to detect all copy number and sequence variants in both index males and carrier females. Assay validation was 100% concordant with other methodologies. A total of 772 samples have been tested, of which 62% (N = 480) were index cases with a clinical suspicion of DMD. Carrier testing females account for 38% (N = 292). Molecular diagnosis was confirmed in 86% (N = 413) of the index cases. Intragenic deletions and duplications (single-exon or multi-exon) were detected in 60% (N = 247) and 14% (N = 58) of the index cases, respectively. Full-sequence analysis of the entire gene allows for detection of deep intronic pathogenic variants and accurate breakpoint detection of CNVs involving similar exons, which could have an impact on the outcome of clinical trials. This comprehensive assay is highly sensitive for diagnostic testing for DMD and is also suitable for confirmatory testing for newborn screening for DMD.

Clinical validation of a new molecular test (Seegene Allplex™ Vaginitis) for the diagnosis of vaginitis: a cross-sectional study

OBJECTIVE

To validate the use of Seegene Allplex™ Vaginitis assay in the diagnosis of candidiasis, bacterial vaginosis (BV) and trichomoniasis.

DESIGN

Cross-sectional, prospective study conducted in a single centre.

SETTING

Outpatient clinic of a gynaecology department.

POPULATION

Consecutive symptomatic and asymptomatic women (18-60 years of age).

METHODS

Comparison of the assay test with the reference standards for the diagnosis of vaginitis (cultures for yeasts, Nugent for BV and nucleic acid amplification test for trichomoniasis).

MAIN OUTCOME MEASURES

Performance of the investigational assay, in comparison with the reference standards for the diagnosis of the presence of Candida spp., Trichomonas vaginalis and BV. Secondary objectives are the evaluation of the performance of the test in postmenopausal women and in symptomatic women.

RESULTS

A diagnosis of vaginitis was established in 14.0%. The global prevalences of BV, Candida spp. and T. vaginalis were 22.3%, 13.2% and 2.4%, respectively. The sensitivity and specificity of the assay test for those three causes of vaginitis were as follows: BV 91.7% and 86.6%; any Candida spp. 91.1% and 95.6%; Candida albicans 88.1% and 98.2%, non-albicans Candida 100% and 97.5%, and T. vaginalis 94.4 and 99.9%. The performance of the test was identical in the subgroup of women that reported vulvovaginal symptoms. The presence of multiple infections did not interfere with the performance of the test.

CONCLUSIONS

The Seegene Allplex™ Vaginitis assay has an excellent performance in the diagnosis of the BV and presence of Candida; the results were good for trichomoniasis, but the study was underpowered for this outcome.

TWEETABLE ABSTRACT

Seegene Allplex™ Vaginitis is an excellent option for screening and diagnosis of vaginitis.