11. Robust saliva-based RNA extraction-free one-step nucleic acid amplification test for mass SARS-CoV-2 monitoringEva Rajh, Tina Šket, Arne Praznik, Petra Sušjan, Alenka Šmid, Dunja Urbančič, Irena Mlinarič-Raščan, Polona Kogovšek, Tina Demšar, Mojca Milavec, Katarina Prosenc, Žiga Jensterle, Mihaela Zidarn, Viktorija Tomič, Gabriele Turel, Tatjana Lejko-Zupanc, Roman Jerala, Mojca Benčina, 2021, izvirni znanstveni članek Povzetek: Early diagnosis with rapid detection of the virus plays a key role in preventing the spread of infection and in treating patients effectively. In order to address the need for a straightforward detection of SARS-CoV-2 infection and assessment of viral spread, we developed rapid, sensitive, extraction-free one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) tests for detecting SARS-CoV-2 in saliva. We analyzed over 700 matched pairs of saliva and nasopharyngeal swab (NSB) specimens from asymptomatic and symptomatic individuals. Saliva, as either an oral cavity swab or passive drool, was collected in an RNA stabilization buffer. The stabilized saliva specimens were heat-treated and directly analyzed without RNA extraction. The diagnostic sensitivity of saliva-based RT-qPCR was at least 95% in individuals with subclinical infection and outperformed RT-LAMP, which had at least 70% sensitivity when compared to NSBs analyzed with a clinical RT-qPCR test. The diagnostic sensitivity for passive drool saliva was higher than that of oral cavity swab specimens (95% and 87%, respectively). A rapid, sensitive one-step extraction-free RT-qPCR test for detecting SARS-CoV-2 in passive drool saliva is operationally simple and can be easily implemented using existing testing sites, thus allowing high-throughput, rapid, and repeated testing of large populations. Furthermore, saliva testing is adequate to detect individuals in an asymptomatic screening program and can help improve voluntary screening compliance for those individuals averse to various forms of nasal collections.
Ključne besede: SARS-CoV-2, COVID-19, COVID-19 serological testing, real-time polymerase chain reaction, saliva, oral cavity swab, passive drool, pooling
Objavljeno v DiRROS: 09.11.2021; Ogledov: 1086; Prenosov: 545
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12. Usefulness of rapid antigen testing for SARS-CoV-2 screening of healthcare workers : ǂa ǂpilot studyAnja Šterbenc, Viktorija Tomič, Urška Bidovec, Katja Vrankar, Aleš Rozman, Mihaela Zidarn, 2021, kratki znanstveni prispevek Povzetek: Background. Identification of infected healthcare workers (HCWs) is an important step in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) transmission control. Rapid antigen tests (RATs) are considered an important addition to molecular tests in diagnosing coronavirus disease 2019 (COVID-19), mainly because of their fast turnaround time, easier analytical procedure and lower price. However, real-life studies on the usefulness of such testing for screening of HCWs are limited. Methods. Physicians, nurses and hospital attendants currently working at the University Clinic of Respiratory and Allergic Diseases Golnik were invited to participate in the pilot study. Nasopharyngeal swabs were obtained three times per week for two consecutive weeks and tested with a point-of-care RAT and reverse transcription polymerase chain reaction (RT-PCR). Serum samples were obtained at the beginning of the study and 2 weeks after the last swab was collected to evaluate the serological status. Results. A total of 191 nasopharyngeal swabs from 36 HCWs were obtained. None of the samples tested was positive for the presence of SARS-CoV-2 antigen, whereas two HCWs tested positive on RT-PCR. Of these, one HCW had a newly identified SARS-CoV-2 infection, whereas RT-PCR probably detected a previous but recent infection in the other HCW. Conclusio.n Based on the results of this pilot study, it is unlikely that RAT will reliably detect novel SARS-CoV-2 infections among asymptomatic HCWs despite serial sampling. Although RT-PCR-based screening of HCWs may not be feasible due to high sample volume, molecular methods may identify SARS-CoV-2-infected HCWs already during the presymptomatic stage.
Ključne besede: SARS-CoV-2, health personnel, COVID-19 serological testing, real-time polymerase chain reaction, rapid antigen test, screening
Objavljeno v DiRROS: 28.05.2021; Ogledov: 1061; Prenosov: 314
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13. Cold urticaria : what we know and what we do not knowNatalya Maltseva, Elena Borzova, Daria Fomina, Mojca Bizjak, Dorothea Terhorst, Mitja Košnik, Kanokvalai Kulthanan, Raisa Meshkova, Simon Francis Thomsen, Marcus Maurer, 2020, izvirni znanstveni članek Povzetek: Cold urticaria (ColdU) is a common form of chronic inducible urticaria characterised by the development of wheals, angioedema or both in response to cold exposure. Recent research and guideline updates have advanced our understanding and management of ColdU. Today, its pathophysiology is thought to involve the cold-induced formation of autoallergens and IgE to these autoallergens, which provoke a release of proinflammatory mediators from skin mast cells. The classification of ColdU includes typical and atypical subtypes. We know that cold-induced wheals usually develop on rewarming and resolve within an hour and that anaphylaxis can occur. The diagnosis relies on the patient's history and cold stimulation testing. Additional diagnostic work-up, including a search for underlying infections, should only be done if indicated by the patient's history. The management of ColdU includes cold avoidance, the regular use of nonsedating antihistamines, and the off-label use of omalizumab. However, many questions regarding ColdU remain unanswered. Here, we review what is known about ColdU, and we present important unanswered questions on the epidemiology, underlying pathomechanisms, clinical heterogeneity and treatment outcomes. Our aim is to guide future efforts that will close these knowledge gaps and advance the management of ColdU.
Ključne besede: urticaria, cryopyrin-associated periodic syndromes, cold-induced urticaria, familial cold autoinflammatory syndrome, cold stimulation testing, wheals, cryoglobulinemic vasculitis, cryoglobulins
Objavljeno v DiRROS: 14.12.2020; Ogledov: 1286; Prenosov: 364
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14. Detection of EGFR variants in plasma : a multilaboratory comparison of a real-time PCR EGFR mutation test in EuropeCleo Keppens, John Palma, Partha Das, Sidney Scudder, Wei Wen, Nicola Normanno, Han J. J. M. van Krieken, Alessandra Sacco, Francesca Fenizia, David Gonzalez de Castro, Selma Hönigschnabl, Izidor Kern, Fernando Lopez-Rios, Maria D. Lozano, Antonio Marchetti, Philippe Halfon, Ed Schuuring, Ulrike Setinek, Boe Sorensen, Phillipe Taniere, Markus Tiemann, Hana Vosmikova, Elisabeth Dequeker, 2018, izvirni znanstveni članek Povzetek: Molecular testing of EGFR is required to predict the response likelihood to targeted therapy in non-small cell lung cancer. Analysis of circulating tumor DNA in plasma may complement limitations of tumor tissue. This study evaluated the interlaboratory performance and reproducibility of a real-time PCR EGFR mutation test (cobas EGFR Mutation Test v2) to detect EGFR variants in plasma. Fourteen laboratories received two identical panels of 27 single-blinded plasma samples. Samples were wild type or spiked with plasmid DNA to contain seven common EGFR variants at six predefined concentrations from 50 to 5000 copies per milliliter. The circulating tumor DNA was extracted by a cell-free circulating DNA sample preparation kit (cobas cfDNA Sample Preparation Kit), followed by duplicate analysis with the real-time PCR EGFR mutation test (Roche Molecular Systems, Pleasanton, CA). Lowest sensitivities were obtained for the c.2156G>C p.(Gly719Ala) and c.2573T>G p.(Leu858Arg) variants for the lowest target copies. For all other variants, sensitivities varied between 96.3% and 100.0%. All specificities were 98.8% to 100.0%. Coefficients of variation indicated good intralaboratory and interlaboratory repeatability and reproducibility but increased for decreasing concentrations. Prediction models revealed a significant correlation for all variants between the predefined copy number and the observed semiquantitative index values, which reflect the samples' plasma mutation load. This study demonstrates an overall robust performance of the real-time PCR EGFR mutation test kit in plasma. Prediction models may be applied to estimate the plasma mutation load for diagnostic or research purposes.
Ključne besede: non-small cell lung cancer, plasma, EGFR, molecular testing
Objavljeno v DiRROS: 23.11.2020; Ogledov: 1368; Prenosov: 271
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15. Management of a surgical patient with a label of penicillin allergy : narrative review and consensus recommendationsLouise C. Savic, David A. Khan, Peter Kopač, Russel C. Clarke, Peter J. Cooke, Pascale Dewachter, Didier G. Ebo, Tomaz Garcez, Lene Heise Garvey, Anne Berit Guttormsen, 2019, pregledni znanstveni članek Povzetek: Unsubstantiated penicillin-allergy labels are common in surgical patients, and can lead to significant harm through avoidance of best first-line prophylaxis of surgical site infections and increased infection with resistant bacterial strains. Up to 98% of penicillin-allergy labels are incorrect when tested. Because of the scarcity of trained allergists in all healthcare systems, only a minority of surgical patients have the opportunity to undergo testing and de-labelling before surgery. Testing pathways can be modified and shortened in selected patients. A variety of healthcare professionals can, with appropriate training and in collaboration with allergists, provide testing for selected patients. We review how patients might be assessed, the appropriate testing strategies that can be used, and the minimum standards of safe testing.
Ključne besede: allergy and immunology, drug hypersensitivity, penicillins, antibiotic prophylaxis, surgery, operative surgical procedures, bacterial infections, surgical wound infection, drug provocation testing, surgical procedures
Objavljeno v DiRROS: 16.10.2020; Ogledov: 1405; Prenosov: 410
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16. The use of drug provocation testing in the investigation of suspected immediate perioperative allergic reactions : current statusLene Heise Garvey, Didier G. Ebo, Mogens Krøigaard, Sinisa Savic, Russel C. Clarke, Peter J. Cooke, Pascale Dewachter, Tomaz Garcez, Anne Berit Guttormsen, Philip M. Hopkins, Peter Kopač, 2019, pregledni znanstveni članek Povzetek: Suspected perioperative allergic reactions are often severe. To avoid potentially life-threatening re-exposure to the culprit drug, establishing a firm diagnosis and identifying the culprit is crucial. Drug provocation tests are considered the gold standard in drug allergy investigation but have not been recommended in the investigation of perioperative allergy, mainly because of the pharmacological effects of drugs such as induction agents and neuromuscular blocking agents. Some specialised centres have reported benefits of provocation testing in perioperative allergy investigation, but the literature on the subject is limited. Here we provide a status update on the use of drug provocation testing in perioperative allergy, including its use in specific drug groups. This review is based on a literature search and experiences of the authors comprising anaesthesiologists and allergists with experience in perioperative allergy investigation. In addition, 19 participating centres in the International Suspected Perioperative Allergic Reaction Group were surveyed on the use of provocation testing in perioperative allergy investigation. A response was received from 13 centres in eight European countries, New Zealand, and the USA. Also, 21 centres from the Australian and New Zealand Anaesthetic Allergy Group were surveyed. Two centres performed provocation routinely and seven centres performed no provocations at all. Nearly half of the centres reported performing provocations with induction agents and neuromuscular blocking agents. Drug provocation testing is being used in perioperative allergy investigation in specialised centres, but collaborations between relevant specialties and multicentre studies are necessary to determine indications and establish common testing protocols.
Ključne besede: allergy and immunology, drug hypersensitivity, anesthesia, drug-related side effects and adverse reactions, anaphylaxis, perioperative period, allergic reactions, hypersensitivity reaction, perioperative anaphylaxis, allergy testing, challenge testing, drug provocation test
Objavljeno v DiRROS: 09.10.2020; Ogledov: 1310; Prenosov: 485
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17. Management of suspected immediate perioperative allergic reactions : an international overview and consensus recommendationsLene Heise Garvey, Pascale Dewachter, David L. Hepner, Paul Michel Mertes, Susanna Voltolini, Russel C. Clarke, Peter J. Cooke, Tomaz Garcez, Anne Berit Guttormsen, Didier G. Ebo, Philip M. Hopkins, Peter Kopač, 2019, pregledni znanstveni članek Povzetek: Suspected perioperative allergic reactions are rare but can be life-threatening. The diagnosis is difficult to make in the perioperative setting, but prompt recognition and correct treatment is necessary to ensure a good outcome. A group of 26 international experts in perioperative allergy (anaesthesiologists, allergists, and immunologists) contributed to a modified Delphi consensus process, which covered areas such as differential diagnosis, management during and after anaphylaxis, allergy investigations, and plans for a subsequent anaesthetic. They were asked to rank the appropriateness of statements related to the immediate management of suspected perioperative allergic reactions. Statements were selected to represent areas where there is a lack of consensus in existing guidelines, such as dosing of epinephrine and fluids, the management of impending cardiac arrest, and reactions refractory to standard treatment. The results of the modified Delphi consensus process have been included in the recommendations on the management of suspected perioperative allergic reactions. This paper provides anaesthetists with an overview of relevant knowledge on the immediate and postoperative management of suspected perioperative allergic reactions based on current literature and expert opinion. In addition, it provides practical advice and recommendations in areas where consensus has been lacking in existing guidelines.
Ključne besede: allergy and immunology, drug hypersensitivity, anesthesia, drug-related side effects and adverse reactions, anaphylaxis, epinephrine, Delphi technique, perioperative period, allergic reactions, hypersensitivity reaction, adrenaline, perioperative anaphylaxis, allergy testing, guideline
Objavljeno v DiRROS: 09.10.2020; Ogledov: 1384; Prenosov: 424
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18. Lung cancer biomarker testing : perspective from EuropeErik Thunnissen, Birgit Weynand, Dalma Udovicic-Gagula, Luka Brčić, Malgorzata Szolkowska, Paul Hofman, Silvana Smojver-Ježek, Sisko Anttila, Fiorella Calabrese, Izidor Kern, 2020, pregledni znanstveni članek Povzetek: A questionnaire on biomarker testing previously used in central European countries was extended and distributed in Western and Central European countries to the pathologists participating at the Pulmonary Pathology Society meeting 26-28 June 2019 in Dubrovnik, Croatia. Each country was represented by one responder. For recent biomarkers the availability and reimbursement of diagnoses of molecular alterations in non-small cell lung carcinoma varies widely between different, also western European, countries. Reimbursement of such assessments varies widely between unavailability and payments by the health care system or even pharmaceutical companies. The support for testing from alternative sources, such as the pharmaceutical industry, is no doubt partly compensating for the lack of public health system support, but it is not a viable or long-term solution. Ideally, a structured access to testing and reimbursement should be the aim in order to provide patients with appropriate therapeutic options. As biomarker enabled therapies deliver a 50% better probability of outcome success, improved and unbiased reimbursement remains a major challenge for the future.
Ključne besede: lung neoplasms -- diagnosis -- therapy -- Europe, lung cancer, predictive testing
Objavljeno v DiRROS: 21.09.2020; Ogledov: 1637; Prenosov: 1054
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19. Next-generation sequencing of drug resistant Mycobacterium tuberculosis clinical isolates in low-incidence countriesEva Sodja, Nataša Toplak, Simon Koren, Minka Kovač, Sara Truden, Biljana Ilievska Poposka, Marija Žolnir-Dovč, 2019, izvirni znanstveni članek Povzetek: Drug resistant tuberculosis (TB), especially multidrug (MDR) and extensively drug-resistant (XDR) TB, is still a serious problem in global TB control. Slovenia and North Macedonia are low-incidence countries with TB incidence rates of 5.4 and 10.4 in 2017, respectively. In both countries, the percentage of drug resistant TB is very low with sporadic cases of MDR-TB. However, global burden of drug-resistant TB continues to increase imposing huge impact on public health systems and strongly stimulating the detection of gene variants related with drug resistance in TB. Next-generation sequencing (NGS) can provide comprehensive analysis of gene variants linked to drug resistance in Mycobacterium tuberculosis. Therefore, the aim of our study was to examine the feasibility of a full-length gene analysis for the drug resistance related genes (inhA, katG, rpoB, embB) using Ion Torrent technology and to compare the NGS results with those obtained from conventional phenotypic drug susceptibility testing (DST) in TB isolates. Between 1996 and 2017, we retrospectively selected 56 TB strains from our National mycobacterial culture collection. Of those, 33 TB isolates from Slovenian patients were isolated from various clinical samples and subjected to phenotypic DST testing in Laboratory for Mycobacteria (University Clinic Golnik, Slovenia). The remaining 23 TB isolates were isolated from Macedonian patients and sent to our laboratory for assistance in phenotypic DST testing. TB strains included were either mono-, poly- or multidrug resistant. For control purposes, we also randomly selected five TB strains susceptible to first-line anti-TB drugs. High concordance between genetic (Ion Torrent technology) and standard phenotypic DST testing for isoniazid, rifampicin and ethambutol was observed, with percent of agreement of 77%, 93.4% and 93.3%, sensitivities of 68.2%, 100% and 100%, and specificities of 100%, 80% and 88.2%, respectively. In conclusion, the genotypic DST using Ion Torrent semiconductor NGS successfully predicted drug resistance with significant shortening of time needed to obtain the resistance profiles from several weeks to just a few days.
Ključne besede: drug resistant tuberculosis, next-generation sequencing, low-incidence countries, phenotypic drug susceptibility testing
Objavljeno v DiRROS: 24.07.2020; Ogledov: 1869; Prenosov: 1052
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