المؤلفون: Charlotte Michel, Fedoua Echahidi, Sammy Place, Lorenzo Filippin, Vincent Colombie, Nicolas Yin, Delphine Martiny, Olivier Vandenberg, Denis Piérard, Marie Hallin

المصدر: Microorganisms, Vol 12, Iss 5, p 857 (2024)

مصطلحات موضوعية: Legionella pneumophila, Legionella pneumophila ST1, whole genome sequencing, genomic typing, wgMLST, cgMLST, Biology (General), QH301-705.5

الوصف: Legionella pneumophila can cause a large panel of symptoms besides the classic pneumonia presentation. Here we present a case of fatal nosocomial cellulitis in an immunocompromised patient followed, a year later, by a second case of Legionnaires’ disease in the same ward. While the first case was easily assumed as nosocomial based on the date of symptom onset, the second case required clear typing results to be assigned either as nosocomial and related to the same environmental source as the first case, or community acquired. To untangle this specific question, we applied core-genome multilocus typing (MLST), whole-genome single nucleotide polymorphism and whole-genome MLST methods to a collection of 36 Belgian and 41 international sequence-type 1 (ST1) isolates using both thresholds recommended in the literature and tailored threshold based on local epidemiological data. Based on the thresholds applied to cluster isolates together, the three methods gave different results and no firm conclusion about the nosocomial setting of the second case could been drawn. Our data highlight that despite promising results in the study of outbreaks and for large-scale epidemiological investigations, next-generation sequencing typing methods applied to ST1 outbreak investigation still need standardization regarding both wet-lab protocols and bioinformatics. A deeper evaluation of the L. pneumophila evolutionary clock is also required to increase our understanding of genomic differences between isolates sampled during a clinical infection and in the environment.

وصف الملف: electronic resource

العلاقة: https://www.mdpi.com/2076-2607/12/5/857Test; https://doaj.org/toc/2076-2607Test

الوصول الحر: https://doaj.org/article/5d562d8ab810480a80b81ac3f5be2f1fTest

المؤلفون: Charlotte Michel, Charlotte Martin, Pierre Smeesters, Jean-Christophe Goffard, Thomas Demuyser, Marie Hallin

المصدر: Frontiers in Medicine, Vol 10 (2023)

مصطلحات موضوعية: Next-Generation Sequencing (NGS), clinical microbiological diagnosis, questionnaire, survey, microbiological diagnosis, Medicine (General), R5-920

الوصف: BackgroundThe translation of Next-Generation Sequencing (NGS) from research to clinical microbiology is increasing rapidly, but its integration into routine clinical care struggles to catch-up. A challenge for clinical laboratories is that the substantial investments made in the required technologies and resources must meet both current and forthcoming needs.MethodsTo get a clinical perspective of these needs, we have sent a survey to infectious diseases clinicians of five hospitals, covering the following topics: NGS knowledge, expected syndromes and patients foreseen to benefit from NGS, and expected impact on antimicrobial prescription.ResultsAccording to clinicians, benefits of NGS are mostly expected in neurological and respiratory infections diagnostics.ConclusionA better dialog between microbiologists and clinicians about hopes and limits of NGS in microbiology may help identifying key investments needed for clinical laboratories, today and tomorrow.

وصف الملف: electronic resource

العلاقة: https://www.frontiersin.org/articles/10.3389/fmed.2023.1225408/fullTest; https://doaj.org/toc/2296-858XTest

الوصول الحر: https://doaj.org/article/7b52e4007ecc4acf8fdb6e4db4be0180Test

المؤلفون: Corentin Deckers, Reza Soleimani, Olivier Denis, Pierre Bogaerts, Catherine Berhin, Hector Rodríguez-Villalobos, Julie Descy, Marie Hallin, Claire Nonhoff, Stefanie Desmet, Koen Magerman, Anne Marie Van den Abeele, Bénédicte Lissoir, Veerle Matheeussen, Kris Vernelen, Te-Din Huang

المصدر: Journal of Global Antimicrobial Resistance, Vol 28, Iss , Pp 125-129 (2022)

مصطلحات موضوعية: Interlaboratory assay, Quality control, Multidrug-resistant organisms, Automated susceptibility testing, Disk diffusion, Microbiology, QR1-502

الوصف: ABSTRACT: Objectives: In order to elaborate a new national challenge panel of resistant Gram-negative bacilli and Gram-positive cocci strains for the validation of routine antimicrobial susceptibility testing (AST) methods, an interlaboratory evaluation was organised. Methods: The results of 12 well-characterised multidrug-resistant strains tested by nine laboratories using local disk diffusion (DD) and automated AST (AUST) methods were compared with the reference broth microdilution method. Results: Overall categorical agreement ranged from 70% to 100% both for DD and AUST and was >90% for all but one strain for all antibiotics. Conclusion: Our multicentre AST study showed good reproducibility and the panel can be used as national resistant reference strains for routine AST validation.

وصف الملف: electronic resource

العلاقة: http://www.sciencedirect.com/science/article/pii/S2213716522000054Test; https://doaj.org/toc/2213-7165Test

الوصول الحر: https://doaj.org/article/f200bed75abd4cfa9291c376e01f1f7cTest

المؤلفون: Valéry Daubie, Houssein Chalhoub, Bob Blasdel, Hafid Dahma, Maya Merabishvili, Tea Glonti, Nathalie De Vos, Johan Quintens, Jean-Paul Pirnay, Marie Hallin, Olivier Vandenberg

المصدر: Frontiers in Cellular and Infection Microbiology, Vol 12 (2022)

مصطلحات موضوعية: phage (bacteriophage), susceptibility, clinical microbiology, diagnosis, personalized medicine, Microbiology, QR1-502

الوصف: As the global burden of disease caused by multidrug resistant bacteria is a major source of concern, credible clinical alternatives to antibiotic therapy, such as personalized phage therapy, are actively explored. Although phage therapy has been used for more than a century, the issue of an easy to implement diagnostic tool for determining phage susceptibility that meets current routine clinical needs is still open. In this Review, we summarize the existing methods used for determining phage activity on bacteria, including the three reference methods: the spot test, the double agar overlay plaque assay, and the Appelmans method. The first two methods rely on the principle of challenging the overnight growth of a lawn of bacteria in an agar matrix to a known relative phage to bacteria concentration and represent good screening tools to determine if the tested phage can be used for a “passive” and or “active” treatment. Beside these methods, several techniques, based on “real-time” growth kinetics assays (GKA) have been developed or are under development. They all monitor the growth of clinical isolates in the presence of phages, but use various detection methods, from classical optical density to more sophisticated techniques such as computer-assisted imagery, flow-cytometry, quantitative real-time polymerase chain reaction (qPCR) or metabolic indicators. Practical considerations as well as information provided about phage activity are reviewed for each technique. Finally, we also discuss the analytical and interpretative requirements for the implementation of a phage susceptibility testing tool in routine clinical microbiology.

وصف الملف: electronic resource

العلاقة: https://www.frontiersin.org/articles/10.3389/fcimb.2022.1000721/fullTest; https://doaj.org/toc/2235-2988Test

الوصول الحر: https://doaj.org/article/ba45576ef127413daba03e7c6a2edb61Test

المؤلفون: Nicolas Yin, Marc Van Nuffelen, Magali Bartiaux, Thierry Préseau, Inge Roggen, Sabrina Delaunoy, Bhavna Mahadeb, Hafid Dahma, Laurent Busson, Olivier Vandenberg, Marie Hallin

المصدر: PLoS ONE, Vol 17, Iss 9, p e0274222 (2022)

مصطلحات موضوعية: Medicine, Science

الوصف: IntroductionUsing respiratory virus rapid diagnostic tests in the emergency department could allow better and faster clinical management. Point-of-care PCR instruments now provide results in less than 30 minutes. The objective of this study was to assess the impact of the use of a rapid molecular diagnostic test, the cobas® Influenza A/B & RSV Assay, during the clinical management of emergency department patients.MethodsPatients (adults and children) requiring admission or suffering from an underlying condition at risk of respiratory complications were prospectively recruited in the emergency department of four hospitals in the Brussels region. Physicians' intentions regarding admission, isolation, antibiotic, and antiviral use were collected before and after performing the rapid molecular test. Additionally, a comparison of the analytical performance of this test against antigen rapid tests and viral culture was performed as well as a time-to-result evaluation.ResultsAmong the 293 patients recruited, 90 had a positive PCR, whereas 44 had a positive antigen test. PCR yielded a sensitivity of 100% for all targets. Antigen tests yielded sensitivities ranging from 66.7% for influenza B to 83.3% for respiratory syncytial virus (RSV). The use of PCR allowed a decrease in the overall need for isolation and treatment by limiting the isolation of negative patients and antibiotic use for positive patients. Meanwhile, antiviral treatments better targeted patients with a positive influenza PCR.ConclusionThe use of a rapid influenza and RSV molecular test improves the clinical management of patients admitted to the emergency department by providing a fast and reliable result. Their additional cost compared to antigen tests should be balanced with the benefit of their analytical performance, leading to efficient reductions in the need for isolation and antibiotic use.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1932-6203Test

الوصول الحر: https://doaj.org/article/7a1797aadd3c4b1b805293e83c091a57Test

المؤلفون: Nicolas Yin, Simon Dellicour, Valery Daubie, Nicolas Franco, Magali Wautier, Christel Faes, Dieter Van Cauteren, Liv Nymark, Niel Hens, Marius Gilbert, Marie Hallin, Olivier Vandenberg

المصدر: Frontiers in Medicine, Vol 8 (2021)

مصطلحات موضوعية: COVID-19, SARS-CoV-2, forecast, epidemic trend, cycle threshold (Ct) value, Medicine (General), R5-920

الوصف: Introduction: We assessed the usefulness of SARS-CoV-2 RT-PCR cycle thresholds (Ct) values trends produced by the LHUB-ULB (a consolidated microbiology laboratory located in Brussels, Belgium) for monitoring the epidemic's dynamics at local and national levels and for improving forecasting models.Methods: SARS-CoV-2 RT-PCR Ct values produced from April 1, 2020, to May 15, 2021, were compared with national COVID-19 confirmed cases notifications according to their geographical and time distribution. These Ct values were evaluated against both a phase diagram predicting the number of COVID-19 patients requiring intensive care and an age-structured model estimating COVID-19 prevalence in Belgium.Results: Over 155,811 RT-PCR performed, 12,799 were positive and 7,910 Ct values were available for analysis. The 14-day median Ct values were negatively correlated with the 14-day mean daily positive tests with a lag of 17 days. In addition, the 14-day mean daily positive tests in LHUB-ULB were strongly correlated with the 14-day mean confirmed cases in the Brussels-Capital and in Belgium with coinciding start, peak, and end of the different waves of the epidemic. Ct values decreased concurrently with the forecasted phase-shifts of the diagram. Similarly, the evolution of 14-day median Ct values was negatively correlated with daily estimated prevalence for all age-classes.Conclusion: We provide preliminary evidence that trends of Ct values can help to both follow and predict the epidemic's trajectory at local and national levels, underlining that consolidated microbiology laboratories can act as epidemic sensors as they gather data that are representative of the geographical area they serve.

وصف الملف: electronic resource

العلاقة: https://www.frontiersin.org/articles/10.3389/fmed.2021.743988/fullTest; https://doaj.org/toc/2296-858XTest

الوصول الحر: https://doaj.org/article/7e45ff94a9e84ab6bebf34ae96674817Test

المؤلفون: Charlotte Michel, Michela Raimo, Vladimir Lazarevic, Nadia Gaïa, Nina Leduc, Christiane Knoop, Marie Hallin, Olivier Vandenberg, Jacques Schrenzel, David Grimaldi, Maya Hites

المصدر: Frontiers in Medicine, Vol 8 (2021)

مصطلحات موضوعية: metagenomics, mollicutes, hyperammonemia, lung trasnplantation, next-generation sequencing, Medicine (General), R5-920

الوصف: Background:Mycoplasma hominis and Ureaplasma spp. are responsible for opportunistic infections in transplant patients, sometimes causing a life-threatening hyperammonemia syndrome. Both pathogens are not identified with standard microbiology techniques, resulting in missed or delayed diagnosis. We present a clinical case that illustrates the added value that next-generation sequencing (NGS) may offer in the diagnosis of respiratory infections in immune-compromised patients.Results: A 55 years-old man with idiopathic pulmonary fibrosis underwent double lung transplantation. He received antibiotic prophylaxis with piperacillin-tazobactam and azythromycin. At day 4 post-transplantation (PTx), the patient presented an acute respiratory distress. A broncho-alveolar lavage (BAL) was performed. At day 5 PTx, the patient presented a status epilepticus due to diffuse cerebral oedema. Serum ammonia concentration was 661 μg/dL. BAL bacterial culture was negative. Because of the clinical presentation, special cultures were performed and identified 100.000 CFU/mL of M. hominis and Ureaplasma spp. and specific PCRs were positive for M. hominis and Ureaplasma parvum. Antibiotic therapy was shifted to therapeutic dose of azithromycin and doxycycline; within 48 h ammonia serum concentrations returned to normal but the coma persisted several weeks, followed by a persistent frontal lobe syndrome. A follow-up BAL was performed on day 11 Ptx. The Mycoplasma/Ureaplasma culture was negative, yet the specific PCRs remained positive. Bacterial culture found 100 CFU/mL of Staphylococcus aureus and viral culture was positive for Herpes Simplex Virus-1. These results were confirmed by metagenomic next-generation sequencing (mNGS). In the bacterial fraction, the majority of reads belonged to Corynebacterium propinquum (34.7%), S. aureus (24.1%) and Staphylococcus epidermidis (17.1%). Reads assigned to M. hominis, Ureaplasma urealyticum and parvum represented 0.71, 0.13, and 0.04% of the bacterial fraction and corresponded to 6.9 × 103, 9.7 × 102, and 3.7 × 102 genome equivalents per mL of BAL fluid, respectively. These results are in favor of a cure of the atypical infection.Conclusions: mNGS offered added diagnostic and quantitative values compared to PCR tests, which can remain positive after resolved infections. The initiation of appropriate antibiotic therapy would have occurred earlier on, possibly resulting in a better clinical outcome if mNGS had been performed in a routine fashion.

وصف الملف: electronic resource

العلاقة: https://www.frontiersin.org/articles/10.3389/fmed.2021.684040/fullTest; https://doaj.org/toc/2296-858XTest

الوصول الحر: https://doaj.org/article/daba8418b6f5415abd49caa58525cc25Test

المؤلفون: Nicolas Yin, Cyril Debuysschere, Marc Decroly, Fatima-Zohra Bouazza, Vincent Collot, Charlotte Martin, Fanny Ponthieux, Hafid Dahma, Marius Gilbert, Magali Wautier, Cecile Duterme, Nathalie De Vos, Marie-Luce Delforge, Stefano Malinverni, Frédéric Cotton, Magali Bartiaux, Marie Hallin

المصدر: Frontiers in Medicine, Vol 8 (2021)

مصطلحات موضوعية: COVID-19, SARS-CoV-2, immunoassay, diagnostic, antigen, PCR, Medicine (General), R5-920

الوصف: Introduction: Since the first wave of COVID-19 in Europe, new diagnostic tools using antigen detection and rapid molecular techniques have been developed. Our objective was to elaborate a diagnostic algorithm combining antigen rapid diagnostic tests, automated antigen dosing and rapid molecular tests and to assess its performance under routine conditions.Methods: An analytical performance evaluation of four antigen rapid tests, one automated antigen dosing and one molecular point-of-care test was performed on samples sent to our laboratory for a SARS-CoV-2 reverse transcription PCR. We then established a diagnostic algorithm by approaching median viral loads in target populations and evaluated the limit of detection of each test using the PCR cycle threshold values. A field performance evaluation including a clinical validation and a user-friendliness assessment was then conducted on the antigen rapid tests in point-of-care settings (general practitioners and emergency rooms) for outpatients who were symptomatic for

وصف الملف: electronic resource

العلاقة: https://www.frontiersin.org/articles/10.3389/fmed.2021.650581/fullTest; https://doaj.org/toc/2296-858XTest

الوصول الحر: https://doaj.org/article/682f6abf2ac74c1f87dfd4a9502bb4b6Test

المؤلفون: Nicolas Dauby, Véronique Yvette Miendje Deyi, Valérie Delforge, Delphine Martiny, Leila Mekkaoui, Marie Hallin, Romain Mahieu, Nathalie Bossuyt, Anne Botteaux, Pierre R. Smeesters

المصدر: International Journal of Infectious Diseases, Vol 81, Iss , Pp 52-56 (2019)

مصطلحات موضوعية: Infectious and parasitic diseases, RC109-216

الوصف: Objectives: The aim was to characterize the clinical features, outcomes, and strain diversity of laboratory-confirmed Streptococcus pyogenes (group A Streptococcus, GAS) infections among inpatients hospitalized at a tertiary level hospital in Brussels, Belgium, according to the patients’ housing status (homeless vs. not homeless). Methods: Between August 2016 and January 2018, all patients hospitalized with a laboratory-confirmed GAS infection were prospectively enrolled and risk factors were recorded. GAS strains were characterized using emm-typing and emm-clustering in both inpatients and outpatients. Analyses were performed according to homelessness status. Results: During the study period, 48% (28/58) of adults hospitalized with a GAS infection at the tertiary hospital were homeless. The estimated incidence rate was 100 times higher for homeless persons. Skin abscesses were more frequent in the homeless group (21.4% vs. 3.3%) and mortality was high (10.7%). Limited emm-type diversity was found in this group, with four emm-types (64, 77, 83, and 101) accounting for 76.1% of the infections, and the majority of these emm-types belonged to the D4 emm-cluster. Pooled analyses of inpatient and outpatient strains indicated lower diversity in the homeless group. Conclusions: The homeless are disproportionately affected by GAS and have a higher rate of abscesses and high mortality. The lower emm-type diversity and preferential infection with four emm-types likely reflects endemic circulation of GAS in this population. Preventive strategies are warranted in this fragile population. Keywords: Streptococcus pyogenes, Epidemiology, Streptococcal m protein, Skin infections, Homeless persons

وصف الملف: electronic resource

العلاقة: http://www.sciencedirect.com/science/article/pii/S1201971219300372Test; https://doaj.org/toc/1201-9712Test

الوصول الحر: https://doaj.org/article/fc5ea268116e43fa9ece5a191d696ee2Test

المؤلفون: Nicolas Yin, Cyril Debuysschere, Valery Daubie, Marc Hildebrand, Charlotte Martin, Sonja Curac, Fanny Ponthieux, Marie-Christine Payen, Olivier Vandenberg, Marie Hallin

المصدر: Diagnostics, Vol 12, Iss 2, p 447 (2022)

مصطلحات موضوعية: SARS-CoV-2, COVID-19, model, diagnostic, test, assay, Medicine (General), R5-920

الوصف: The Lumipulse® G SARS-CoV-2 Ag assay performance was evaluated on prospectively collected saliva and nasopharyngeal swabs (NPS) of recently ill in- and outpatients and according to the estimated viral load. Performances were calculated using RT-PCR positive NPS from patients with symptoms ≤ 7 days and RT-PCR negative NPS as gold standard. In addition, non-selected positive NPS were analyzed to assess the performances on various viral loads. This assay yielded a sensitivity of 93.1% on NPS and 71.4% on saliva for recently ill patients. For NPS with a viral load > 103 RNA copies/mL, sensitivity was 96.4%. A model established on our daily routine showed fluctuations of the performances depending on the epidemic trends but an overall good negative predictive value. Lumipulse® G SARS-CoV-2 assay yielded good performance for an automated antigen detection assay on NPS. Using it for the detection of recently ill patients or to screen high-risk patients could be an interesting alternative to the more expensive RT-PCR.

وصف الملف: electronic resource

العلاقة: https://www.mdpi.com/2075-4418/12/2/447Test; https://doaj.org/toc/2075-4418Test

الوصول الحر: https://doaj.org/article/1545ccad29c64dfe9a193c3bdb58bd6fTest