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3. The assessment of single nucleotide polymorphisms in the ß-tubulin genes in human soil-transmitted helminths exposed to different pressure with benzimidazole drugs

Author

Levecke, Bruno, primary, Rashwan, Nour, additional, Cools, Piet, additional, Albonico, Marco, additional, Ame, Shaali M, additional, Ayana, Mio, additional, Dana, Daniel, additional, Keiser, Jennifer, additional, Montresor, Antonio, additional, Mekonnen, Zeleke, additional, Roose, Sara, additional, Sayasone, Somphou, additional, Vercruysse, Jozef, additional, Verweij, Jaco J, additional, Vlaminck, Johnny, additional, and Prichard, Roger, additional

Published
2024
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4. Self-testing for the detection of SARS-CoV-2 infection with rapid antigen tests for people with suspected COVID-19 in the community

Author

Stohr, Joep J.J.M., Zwart, Vivian F., Goderski, Gabriel, Meijer, Adam, Nagel-Imming, Carla R.S., Kluytmans-van den Bergh, Marjolein F.Q., Pas, Suzan D., van den Oetelaar, Femke, Hellwich, Marloes, Gan, Kim H., Rietveld, Ariene, Verweij, Jaco J., Murk, Jean-Luc, van den Bijllaardt, Wouter, and Kluytmans, Jan A.J.W.

Published
2022
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5. Epidemiological and clinical insights into the enterovirus D68 upsurge in Europe 2021/22 and the emergence of novel B3-derived lineages, ENPEN multicentre study

Author

Simoes, Margarida Pires, primary, Hodcroft, Emma B, additional, Simmonds, Peter, additional, Albert, Jan, additional, Alidjinou, Enagon K, additional, Ambert-Balay, Katia, additional, Andrés, Cristina, additional, Antón, Andrés, additional, Auvray, Christelle, additional, Bailly, Jean-Luc, additional, Baldanti, Fausto, additional, Bastings, Capser, additional, Beard, Stuart, additional, Pereira, Carla Berengua, additional, Berginc, Natasa, additional, Bloemen, Mandy, additional, Blomqvist, Soile, additional, Bosma, Froukje, additional, Böttcher, Sindy, additional, Bubba, Laura, additional, Buderus, Stafan, additional, Cabrerizo, Maria, additional, Calvo, Christina, additional, Celma, Christina, additional, Ceriotti, Ferruccio, additional, Clark, Gemma, additional, Costa, Inës, additional, Coste-Burel, Marianne, additional, Couderé, Karen, additional, Cremer, Jeroen, additional, del Cuerpo Casas, Margarita, additional, Daehne, Theo, additional, de Beer, Jessica, additional, de Ceano-Vivas, Maria, additional, De Gascun, Cillian, additional, de Rougemont, Alexis, additional, Dean, Johnathan, additional, Dembinski, Jennifer L, additional, Diedrich, Sabine, additional, Diez-Domingo, Javier, additional, Dillner, Lena, additional, Dorenberg, Dagny H, additional, Ducancelle, Alexandra, additional, Dudman, Susanne, additional, Dyrdak, Robert, additional, Eis-Huebinger, Anna-Maria, additional, Falces-Romero, Iker, additional, Farkas, Agnes, additional, Feeney, Susan, additional, Fernandez-Garcia, Maria D, additional, Flipse, Jacky, additional, Franck, Kristina T, additional, Galli, Cristina, additional, Garrigue, Isabelle, additional, Geeraedts, Felix, additional, Georgieva, Irina, additional, Giardina, Federica, additional, Guiomar, Raquel, additional, Hauzenberger, Elenor, additional, Heikens, Esther, additional, Henquell, Cécille, additional, Hober, Didier, additional, Hönemann, Amrio, additional, Howson-Wells, Hannah, additional, Hruškar, Željka, additional, Ikonen, Niina, additional, Imbert, Berthemarie, additional, Jansz, Arjan R, additional, Jeannoël, Marion, additional, Jiřincová, Helena, additional, Josset, Laurence, additional, Keeren, Kathrin, additional, Kramer-Lindhout, Naomie, additional, Krokstad, Sidsel, additional, Lazrek, Mouna, additional, Le Guillou-Guillemette, Hélène, additional, Lefeuvre, Caroline, additional, Lind, Andreas, additional, Lunar, Maja M, additional, Maier, Melanie, additional, Marque-Juillet, Stéphanie, additional, McClure, C Patrick, additional, McKenna, James, additional, Meijer, Adam, additional, Menasalvas Ruiz, Ana, additional, Mengual-Chuliá, Beatriz, additional, Midgley, Sofie, additional, Mirand, Audrey, additional, Molenkamp, Richard, additional, Montes, Milagrosa, additional, Moreno-Docón, Antonio, additional, Morley, Ursula, additional, Murk, Jean-Luc, additional, Navascués-Ortega, Ana, additional, Nijhuis, Roel, additional, Nikolaeva-Glomb, Lubomira, additional, Nordbø, Svein A, additional, Numanovic, Sanela, additional, Oggioni, Massimo, additional, Oñate Vergara, Eider, additional, Pacaud, Jordi, additional, Pacreau, Marie L, additional, Panning, Marcus, additional, Pariani, Elena, additional, Pekova, Lili, additional, Pellegrinelli, Laura, additional, Petrovec, Miroslav, additional, Pietsch, Corinna, additional, Pilorge, Léa, additional, Piñeiro, Luis, additional, Piralla, Antonio, additional, Poljak, Mario, additional, Prochazka, Birgit, additional, Rabella, Nuria, additional, Rahamat-Langendoen, Janette C, additional, Rainetova, petra, additional, Reynders, Marijke, additional, Riezebos-Brilman, Annelies, additional, Roorda, Lieuwe, additional, Savolainen-Kopra, Carita, additional, Schuffenecker, Isabelle, additional, Smeets, Leo C, additional, Stoyanova, Ayse, additional, Stefic, Karl, additional, Swanink, Caroline, additional, Tabain, Irena, additional, Tjhie, Jeroen, additional, Thouault, Luc, additional, Tumiotto, Camille, additional, Uceda Renteria, Sara, additional, Uršič, Tina, additional, Vallet, Sophie, additional, Van Ranst, Marc, additional, Van Wunnik, Peter, additional, Verweij, Jaco J, additional, Vila, Jorgina, additional, Wintermans, Bas, additional, Wollants, Elke, additional, Wolthers, Katja C, additional, Xavier López-Labrado, F, additional, Fischer, Thea Kolsen, additional, Harvala, Heli, additional, and Benschop, Kimberley S M, additional

Published
2024
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7. Detection of soil-transmitted helminths and Schistosoma spp. by nucleic acid amplification test:Results of the first 5 years of the only international external quality assessment scheme

Author

Schutte, Annemiek H.J., Koelewijn, Rob, Ajjampur, Sitara S.R., Levecke, Bruno, McCarthy, James S., Mejia, Rojelio, Williams, Steven A., Verweij, Jaco J., van Lieshout, Lisette, van Hellemond, Jaap J., Schutte, Annemiek H.J., Koelewijn, Rob, Ajjampur, Sitara S.R., Levecke, Bruno, McCarthy, James S., Mejia, Rojelio, Williams, Steven A., Verweij, Jaco J., van Lieshout, Lisette, and van Hellemond, Jaap J.

Abstract

BACKGROUND:Infections with soil-transmitted helminths (STH) and schistosomiasis (SCH) result in a significant global health burden, particularly in rural communities in low and middle-income countries. While microscopy remains the primary diagnostic method for STH and SCH in resource-limited settings, nucleic acid amplification tests (NAATs) are gaining prominence as tools for evaluation of public health control programs in endemic countries, and individual diagnosis in high-income countries. Despite the high sensitivity and specificity of NAATs, previous research has highlighted inter-laboratory variations, both in technical and clinical performance, justifying the need for continuous proficiency testing.METHODOLOGY: Results from 5 rounds over a 5-year period of the so far only longitudinal international Helminth External Molecular Quality Assessment Scheme (HEMQAS), coordinated by the Dutch Foundation for Quality Assessment in Medical Laboratories (SKML), were examined in order to (i) assess the diagnostic proficiency of laboratories in detecting helminths in stool and (ii) identify potential factors contributing to variations in performance. OUTCOME AND CONCLUSIONS: Thirty-six laboratories, from 18 countries and 5 continents, participated in HEMQAS. The overall diagnostic performances were satisfying, with remarkably low numbers (<2%) of false-positive results. False-negative results were more often reported for stool (15%) than for DNA (5%) samples. False-negative results varied largely between targets (the highest number (29%) for Trichuris trichiura). Twenty-five laboratories provided a sufficient number of results for a robust comparison between participating laboratories, which confirmed substantial inter-laboratory variability in quantitative NAAT results (Cq-values). This variability likely arises from differences in pre-treatment, DNA isolation and DNA-target amplification procedures. This stud

Published
2024

8. High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment

Author

Sluimer, John, van den Akker, Willem M.R., Goderski, Gabriel, Swart, Arno, van der Veer, Bas, Cremer, Jeroen, Chung, Ngoc Hoa, Molenkamp, Richard, Voermans, Jolanda, Guldemeester, Judith, van der Eijk, Annemiek, de Jong, Menno D., Mithoe, Glen, Hermans, Mirjam H.A., de Beer, Jessica L., Wessels, Els, von Wintersdorff, Christian, Pas, Suzan, Verweij, Jaco J., Melchers, Willem J.G., van de Bovenkamp, Jeroen H.B., Vahidnia, Ali, Gard, Lilli, Schuurman, Rob, Wintermans, Bas, Leversteijn-van Hall, Maurine, Smits, Paul, de Groot, Theun, Deiman, Birgit A.L.M., Bart, Aldert, van der Reijden, Wil, Svraka-Latifovic, Sanela, van der Zanden, Adri G.M., Thijsen, Steven, Schubbert, Rainer, Dreesens, Lisa L., van Duijn, Gert, Ong, David S.Y., Oostra, Monique, Bruisten, Sylvia, van Trijp, Marijke, Pettersson, Annika, van Burgel, Nathalie D., Oudbier, Joke, van der Linden, Michael, Rossen, John, Smit, Pieter, Thai, Khoa, Eggink, Dirk, Meijer, Adam, Sluimer, John, van den Akker, Willem M.R., Goderski, Gabriel, Swart, Arno, van der Veer, Bas, Cremer, Jeroen, Chung, Ngoc Hoa, Molenkamp, Richard, Voermans, Jolanda, Guldemeester, Judith, van der Eijk, Annemiek, de Jong, Menno D., Mithoe, Glen, Hermans, Mirjam H.A., de Beer, Jessica L., Wessels, Els, von Wintersdorff, Christian, Pas, Suzan, Verweij, Jaco J., Melchers, Willem J.G., van de Bovenkamp, Jeroen H.B., Vahidnia, Ali, Gard, Lilli, Schuurman, Rob, Wintermans, Bas, Leversteijn-van Hall, Maurine, Smits, Paul, de Groot, Theun, Deiman, Birgit A.L.M., Bart, Aldert, van der Reijden, Wil, Svraka-Latifovic, Sanela, van der Zanden, Adri G.M., Thijsen, Steven, Schubbert, Rainer, Dreesens, Lisa L., van Duijn, Gert, Ong, David S.Y., Oostra, Monique, Bruisten, Sylvia, van Trijp, Marijke, Pettersson, Annika, van Burgel, Nathalie D., Oudbier, Joke, van der Linden, Michael, Rossen, John, Smit, Pieter, Thai, Khoa, Eggink, Dirk, and Meijer, Adam

Abstract

A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.

Published
2024

9. Detection of soil-transmitted helminths and Schistosoma spp. by nucleic acid amplification test: Results of the first 5 years of the only international external quality assessment scheme.

Author

Schutte, Annemiek H. J., Koelewijn, Rob, Ajjampur, Sitara S. R., Levecke, Bruno, McCarthy, James S., Mejia, Rojelio, Williams, Steven A., Verweij, Jaco J., van Lieshout, Lisette, and van Hellemond, Jaap J.

Subjects
NUCLEIC acid amplification techniques, NUCLEIC acid isolation methods, RESOURCE-limited settings, MEDICAL laboratories, HUMAN DNA, HELMINTHS
Abstract

Background: Infections with soil-transmitted helminths (STH) and schistosomiasis (SCH) result in a significant global health burden, particularly in rural communities in low and middle-income countries. While microscopy remains the primary diagnostic method for STH and SCH in resource-limited settings, nucleic acid amplification tests (NAATs) are gaining prominence as tools for evaluation of public health control programs in endemic countries, and individual diagnosis in high-income countries. Despite the high sensitivity and specificity of NAATs, previous research has highlighted inter-laboratory variations, both in technical and clinical performance, justifying the need for continuous proficiency testing. Methodology: Results from 5 rounds over a 5-year period of the so far only longitudinal international Helminth External Molecular Quality Assessment Scheme (HEMQAS), coordinated by the Dutch Foundation for Quality Assessment in Medical Laboratories (SKML), were examined in order to (i) assess the diagnostic proficiency of laboratories in detecting helminths in stool and (ii) identify potential factors contributing to variations in performance. Outcome and conclusions: Thirty-six laboratories, from 18 countries and 5 continents, participated in HEMQAS. The overall diagnostic performances were satisfying, with remarkably low numbers (<2%) of false-positive results. False-negative results were more often reported for stool (15%) than for DNA (5%) samples. False-negative results varied largely between targets (the highest number (29%) for Trichuris trichiura). Twenty-five laboratories provided a sufficient number of results for a robust comparison between participating laboratories, which confirmed substantial inter-laboratory variability in quantitative NAAT results (Cq-values). This variability likely arises from differences in pre-treatment, DNA isolation and DNA-target amplification procedures. This study emphasizes the complexity of molecular diagnosis for STH and SCH, highlighting the critical role of proper stool preparation and DNA isolation methods. The results underscore the necessity for laboratory professionals and public health decision-makers to recognize these complexities and continuously undertake external quality assessment schemes to ensure accurate and reliable performance in molecular diagnosis. Author summary: Parasitic worms cause significant global health challenges, particularly in rural communities in low and middle-income countries. Laboratory tests that detect parasite DNA in human stool are increasingly being used for the diagnosis of parasitic worm infections. While parasite DNA detection can be an excellent diagnostic tool, its performance in clinical practice varies considerably, as demonstrated by previous research. To ensure the quality in diagnostic testing of these parasitic worms, it is important that laboratories evaluate the diagnostic performance of their DNA-based tests by participating in a so-called external quality assessment scheme (EQAS). This study, focusing on the first five-yearly rounds of the so far only longitudinal international EQAS to date, reveals that quantitative DNA detection results are not directly comparable across laboratories due to substantial inter-laboratory variability. This variability mainly stems from differences in pre-treatment and DNA isolation protocols, and to a lesser extent from differences in DNA target amplification procedures. Furthermore, the study underscores the complexity of molecular diagnosis for parasitic worms in clinical practice and the necessity for laboratories to engage in EQAs to guarantee the proper functioning of these diagnostic tests. [ABSTRACT FROM AUTHOR]

Published
2024
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10. COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study

Author

Sikkema, Reina S, Pas, Suzan D, Nieuwenhuijse, David F, O'Toole, Áine, Verweij, Jaco, van der Linden, Anne, Chestakova, Irina, Schapendonk, Claudia, Pronk, Mark, Lexmond, Pascal, Bestebroer, Theo, Overmars, Ronald J, van Nieuwkoop, Stefan, van den Bijllaardt, Wouter, Bentvelsen, Robbert G, van Rijen, Miranda M L, Buiting, Anton G M, van Oudheusden, Anne J G, Diederen, Bram M, Bergmans, Anneke M C, van der Eijk, Annemiek, Molenkamp, Richard, Rambaut, Andrew, Timen, Aura, Kluytmans, Jan A J W, Oude Munnink, Bas B, Kluytmans van den Bergh, Marjolein F Q, and Koopmans, Marion P G

Published
2020
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11. The incidence, aetiology, and adverse clinical consequences of less severe diarrhoeal episodes among infants and children residing in low-income and middle-income countries: a 12-month case-control study as a follow-on to the Global Enteric Multicenter Study (GEMS)

Author

Kotloff, Karen L, Nasrin, Dilruba, Blackwelder, William C, Wu, Yukun, Farag, Tamer, Panchalingham, Sandra, Sow, Samba O, Sur, Dipika, Zaidi, Anita K M, Faruque, Abu S G, Saha, Debasish, Alonso, Pedro L, Tamboura, Boubou, Sanogo, Doh, Onwuchekwa, Uma, Manna, Byomkesh, Ramamurthy, Thandavarayan, Kanungo, Suman, Ahmed, Shahnawaz, Qureshi, Shahida, Quadri, Farheen, Hossain, Anowar, Das, Sumon K, Antonio, Martin, Hossain, M Jahangir, Mandomando, Inacio, Acácio, Sozinho, Biswas, Kousick, Tennant, Sharon M, Verweij, Jaco J, Sommerfelt, Halvor, Nataro, James P, Robins-Browne, Roy M, and Levine, Myron M

Published
2019
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12. Development and validation of a high-throughput qPCR platform for the detection of soil-transmitted helminth infections

Author

Pilotte, Nils, primary, Omballa, Victor, additional, Padgett, Leah, additional, Manuel, Malathi, additional, Goodman, Jeanne L, additional, Littlewood, Tim, additional, Manoharan, Zayina Zondervenni, additional, van Lieshout, Lisette, additional, Verweij, Jaco, additional, Sekar, Manigandan, additional, Muthukumar, Ajith Kumar, additional, Walch, Gretchen, additional, Gonzalez, Andrew, additional, Galagan, Sean R, additional, Ajjampur, Sitara Swarna Rao, additional, Ibikoule, Moudachirou, additional, Williams, Steven A, additional, Rains, Doug, additional, Dadwal, Ushashi, additional, and Walson, Judd L, additional

Published
2023
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14. First description and phylogenetic analysis of coxsackie virus A non‐polio enteroviruses and parechoviruses A in South Sudanese children

Author

Couderé, Karen, primary, Benschop, Kimberley, additional, van Steen, Astrid, additional, Verweij, Jaco J., additional, Pas, Suzan, additional, Cremer, Jeroen, additional, Edridge, Arthur W. D., additional, Abd‐Elfarag, Gasim O. E., additional, van Hensbroek, Michaël B., additional, Pajkrt, Dasja, additional, Murk, Jean‐Luc, additional, and Wolthers, Katja C., additional

Published
2023
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16. The Novodiag® Stool parasites assay, an innovative high-plex technique for fast detection of protozoa, helminths and microsporidia in stool samples: a retrospective and prospective study

Author

Hartuis Sophie, Lavergne Rose-Anne, Nourrisson Céline, Verweij Jaco, Desoubeaux Guillaume, Lussac-Sorton Florian, Lemoine Jean-Philippe, Cateau Estelle, Jeddi Fakhri, Poirier Philippe, Le Pape Patrice, and Morio Florent

Subjects
stool, gastrointestinal parasites, microscopy, novodiag® stool parasites, high-plex detection, prospective study, comparative evaluation, Infectious and parasitic diseases, RC109-216
Abstract

Objectives: We provide the first evaluation of the CE-IVD marked Novodiag® stool parasites assay (NVD), allowing rapid and high-plex detection of 26 distinct targets, encompassing protozoans, helminths and microsporidia in stool samples. Methods: A total of 254 samples (n = 205 patients) were prospectively processed by the NVD and our routine procedure (RP). Performances of the NVD were compared with RP. Samples only positive by the NVD assay were investigated by external PCR assays. Sensitivity and specificity (Se/Sp) and time from sample receipt to results were determined for each method. The NVD was also evaluated against 77 additional samples positive for a wide range of parasites. Results: Overall positivity rate was 16.9% for RP compared with 34% using the NVD assay, and 164 samples (66%) were negative by both methods. Only 30 positive samples (12%) showed full concordance between RP and NVD. Fifty-three discordant samples were sent for external investigations. Except for Giardia intestinalis and Trichuris spp., higher Se was observed for the NVD assay for Blastocystis spp. (100% vs. 63%), Dientamoeba fragilis (100% vs. 0%), Schistosoma spp. (100% vs. 17%), and Enterobius vermicularis (100% vs. 67%) but roughly similar to RP for the remaining parasites tested. False-positive results were identified for Blastocystis spp., G. intestinalis, and Trichuris spp. using the NVD assay. The NVD mostly provides a diagnosis on the day of sample receipt compared with a mean of three days with RP. Conclusions: Besides some limitations, the NVD is a new diagnostic strategy allowing rapid and high-plex detection of gastrointestinal parasites from unpreserved stools.

Published
2022
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17. Parasitic, bacterial, viral, immune-mediated, metabolic and nutritional factors associated with nodding syndrome

Author

Edridge, Arthur W.D., Abd-Elfarag, Gasim, Deijs, Martin, Broeks, Melissa H., Cristella, Cosimo, Sie, Brandon, Vaz, Frédéric, Jans, Judith, Calis, Job, Verhoef, Hans, Demir, Ayse, Poppert, Sven, Nickel, Beatrice, van Dam, Alje, Sebit, Boy, Titulaer, Maarten, Verweij, Jaco, de Jong, Menno, van Gool, Tom, Faragher, Brian, Verhoeven-Duif, Nanda, Elledge, Stephen, van der Hoek, Lia, van Hensbroek, Michael, Edridge, Arthur W.D., Abd-Elfarag, Gasim, Deijs, Martin, Broeks, Melissa H., Cristella, Cosimo, Sie, Brandon, Vaz, Frédéric, Jans, Judith, Calis, Job, Verhoef, Hans, Demir, Ayse, Poppert, Sven, Nickel, Beatrice, van Dam, Alje, Sebit, Boy, Titulaer, Maarten, Verweij, Jaco, de Jong, Menno, van Gool, Tom, Faragher, Brian, Verhoeven-Duif, Nanda, Elledge, Stephen, van der Hoek, Lia, and van Hensbroek, Michael

Abstract

Nodding syndrome is a neglected, disabling and potentially fatal epileptic disorder of unknown aetiology affecting thousands of individuals mostly confined to Eastern sub-Saharan Africa. Previous studies have identified multiple associations—including Onchocerca volvulus, antileiomodin-1 antibodies, vitamin B6 deficiency and measles virus infection—yet, none is proven causal. We conducted a case-control study of children with early-stage nodding syndrome (symptom onset <1 year). Cases and controls were identified through a household survey in the Greater Mundri area in South Sudan. A wide range of parasitic, bacterial, viral, immune-mediated, metabolic and nutritional risk factors was investigated using conventional and state-of-the-art untargeted assays. Associations were examined by multiple logistic regression analysis, and a hypothetical causal model was constructed using structural equation modelling. Of 607 children with nodding syndrome, 72 with early-stage disease were included as cases and matched to 65 household- and 44 community controls. Mansonella perstans infection (odds ratio 7.04, 95% confidence interval 2.28–21.7), Necator americanus infection (odds ratio 2.33, 95% confidence interval 1.02–5.3), higher antimalarial seroreactivity (odds ratio 1.75, 95% confidence interval 1.20–2.57), higher vitamin E concentration (odds ratio 1.53 per standard deviation increase, 95% confidence interval 1.07–2.19) and lower vitamin B12 concentration (odds ratio 0.56 per standard deviation increase, 95% confidence interval 0.36–0.87) were associated with higher odds of nodding syndrome. In a structural equation model, we hypothesized that Mansonella perstans infection, higher vitamin E concentration and fewer viral exposures increased the risk of nodding syndrome while lower vitamin B12 concentration, Necator americanus and malaria infections resulted from having nodding syndrome. We found no evidence that Onchocerca volvulus, antileiomodin-1 antibodies, vitamin B6 an

Published
2023

18. Severe neonatal enterovirus infection in twins with different outcomes:A case report

Author

Storm, Kelly K., De Herdt, Daan, Couderé, Karen, Verweij, Jaco J., Torn, Leo, Hundscheid, Tim, van Wering, Herbert M., Storm, Kelly K., De Herdt, Daan, Couderé, Karen, Verweij, Jaco J., Torn, Leo, Hundscheid, Tim, and van Wering, Herbert M.

Abstract

Enteroviruses are among the most common causes of acute viral illness worldwide, and in neonates, the clinical course of these infections is heterogeneous. Severe complications, such as myocarditis, are associated with high mortality rates. In this case report, we present the clinical course of premature twins born at 35 weeks of gestational age, suffering from a severe neonatal enterovirus infection with cardiac involvement, which proved fatal in one of the twins. This course led to prompt identification in the other twin and facilitated timely transfer to a neonatal intensive care unit with neonatal hemodynamic expertise, and facilitated the timely transfer to a neonatal intensive care nit with hemodynamic expertise and immediate availability of AZCMO would it have been indicated. Early supportive therapy in the other twin contributed to a positive outcome. Therefore, we emphasize the importance of early recognition in averting adverse consequences. As a recommendation, we propose routine screening of enterovirus in viral panels for febrile newborns.

Published
2023

19. Elevated risk of infection with SARS-CoV-2 Beta, Gamma, and Delta variants compared with Alpha variant in vaccinated individuals

Author

Andeweg, Stijn P., Vennema, Harry, Veldhuijzen, Irene, Smorenburg, Naomi, Schmitz, Dennis, Zwagemaker, Florian, Van Gageldonk-Lafeber, Arianne B., Hahne, Susan J.M., Reusken, Chantal, Knol, Mirjam J., Eggink, Dirk, Schinkel, Janke, Welkers, Matthijs R.A., Jonges, Marcel, Koopsen, Jelle, Jong, Menno D.de, Molenkamp, Richard, Nieuwenhuijse, David F., Sikkema, Reina S., Munnink, Bas B.Oude, Koopmans, Marion, van der Zanden, Adri, Manrho, Laura, Beer, Jessica de, Boers, Stefan A., Meijers, Erin, Vreeswijk, Tom, Sidorov, Igor A., Dunk, Djoo, Smit, Pieter W., Pas, Suzan D., Verweij, Jaco J., Stohr, Joep J.J.M., Dingemans, Jozef, Veer, Brian van der, Alphen, Lieke van, Savelkoul, Paul, Niesters, Hubert G.M., Forero, Erley F.Lizarazo, Fliss, Monika A., Gard, Lilli, Tanja, Anniek A.N., Schuurman10, Rob, Wensing, Annemarie M.J., Hofstra, L. Marije, Wertheim, Heiman F.L., Faber, Timor, Kroneman, Annelies, Mulder, Maarten, Schipper, Maarten, Andeweg, Stijn P., Vennema, Harry, Veldhuijzen, Irene, Smorenburg, Naomi, Schmitz, Dennis, Zwagemaker, Florian, Van Gageldonk-Lafeber, Arianne B., Hahne, Susan J.M., Reusken, Chantal, Knol, Mirjam J., Eggink, Dirk, Schinkel, Janke, Welkers, Matthijs R.A., Jonges, Marcel, Koopsen, Jelle, Jong, Menno D.de, Molenkamp, Richard, Nieuwenhuijse, David F., Sikkema, Reina S., Munnink, Bas B.Oude, Koopmans, Marion, van der Zanden, Adri, Manrho, Laura, Beer, Jessica de, Boers, Stefan A., Meijers, Erin, Vreeswijk, Tom, Sidorov, Igor A., Dunk, Djoo, Smit, Pieter W., Pas, Suzan D., Verweij, Jaco J., Stohr, Joep J.J.M., Dingemans, Jozef, Veer, Brian van der, Alphen, Lieke van, Savelkoul, Paul, Niesters, Hubert G.M., Forero, Erley F.Lizarazo, Fliss, Monika A., Gard, Lilli, Tanja, Anniek A.N., Schuurman10, Rob, Wensing, Annemarie M.J., Hofstra, L. Marije, Wertheim, Heiman F.L., Faber, Timor, Kroneman, Annelies, Mulder, Maarten, and Schipper, Maarten

Abstract

The extent to which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) break through infection- or vaccine-induced immunity is not well understood. We analyzed 28,578 sequenced SARS-CoV-2 samples from individuals with known immune status obtained through national community testing in the Netherlands from March to August 2021. We found evidence of an increased risk of infection by the Beta (B.1.351), Gamma (P.1), or Delta (B.1.617.2) variants compared with the Alpha (B.1.1.7) variant after vaccination. No clear differences were found between vaccines. However, the effect was larger in the first 14 to 59 days after complete vaccination compared with ≥60 days. In contrast to vaccine-induced immunity, there was no increased risk for reinfection with Beta, Gamma, or Delta variants relative to the Alpha variant in individuals with infection-induced immunity.

Published
2023

20. Parasitic, bacterial, viral, immune-mediated, metabolic and nutritional factors associated with nodding syndrome

Author

Genetica Sectie Metabole Diagnostiek, Cancer, Brain, Child Health, LKCH Staf Patiëntenzorg, Genetica, Edridge, Arthur W D, Abd-Elfarag, Gasim, Deijs, Martin, Broeks, Melissa H, Cristella, Cosimo, Sie, Brandon, Vaz, Frédéric M, Jans, Judith J M, Calis, Job, Verhoef, Hans, Demir, Ayse, Poppert, Sven, Nickel, Beatrice, van Dam, Alje, Sebit, Boy, Titulaer, Maarten J, Verweij, Jaco J, de Jong, Menno D, van Gool, Tom, Faragher, Brian, Verhoeven-Duif, Nanda M, Elledge, Stephen J, van der Hoek, Lia, Boele van Hensbroek, Michael, Genetica Sectie Metabole Diagnostiek, Cancer, Brain, Child Health, LKCH Staf Patiëntenzorg, Genetica, Edridge, Arthur W D, Abd-Elfarag, Gasim, Deijs, Martin, Broeks, Melissa H, Cristella, Cosimo, Sie, Brandon, Vaz, Frédéric M, Jans, Judith J M, Calis, Job, Verhoef, Hans, Demir, Ayse, Poppert, Sven, Nickel, Beatrice, van Dam, Alje, Sebit, Boy, Titulaer, Maarten J, Verweij, Jaco J, de Jong, Menno D, van Gool, Tom, Faragher, Brian, Verhoeven-Duif, Nanda M, Elledge, Stephen J, van der Hoek, Lia, and Boele van Hensbroek, Michael

Published
2023

21. Community deworming alleviates geohelminth-induced immune hyporesponsiveness

Author

Wammes, Linda J., Hamid, Firdaus, Wiria, Aprilianto Eddy, May, Linda, Kaisar, Maria M. M., Prasetyani-Gieseler, Margaretta A., Djuardi, Yenny, Wibowo, Heri, Kruize, Yvonne C. M., Verweij, Jaco J., de Jong, Sanne E., Tsonaka, Roula, Houwing-Duistermaat, Jeanine J., Sartono, Erliyani, Luty, Adrian J. F., Supali, Taniawati, and Yazdanbakhsh, Maria

Published
2016

22. Schistosoma mansoni‐specific immune responses and allergy in Uganda

Author

Nkurunungi, G., Kabagenyi, J., Nampijja, M., Sanya, R. E., Walusimbi, B., Nassuuna, J., Webb, E. L., Elliott, A. M., Mpairwe, Harriet, O’Hara, Geraldine, Nerima, Barbara, Kizito, Dennison, Tushabe, John Vianney, Verweij, Jaco, Cose, Stephen, Wammes, Linda, Kabuubi, Prossy, Niwagaba, Emmanuel, Oduru, Gloria, Kabami, Grace, Abayo, Elson, Ssebagala, Eric, Muwonge, Fred, Spaans, Remy Hoek, Muhangi, Lawrence, Lubyayi, Lawrence, Akurut, Helen, Nalukenge, Fatuma, Mirembe, Beatrice, Okello, Justin, Owilla, Sebastian, Levin, Jonathan, Nash, Stephen, Zziwa, Christopher, Nakazibwe, Esther, Tumusiime, Josephine, Ninsiima, Caroline, Amongi, Susan, Kamukama, Grace, Iwala, Susan, Akello, Mirriam, Kizindo, Robert, Sewankambo, Moses, Nsubuga, Denis, Tumwesige, Edward, Abiriga, David, Walusimbi, Richard, Nannozi, Victoria, Kabonesa, Cynthia, Kaweesa, James, Tukahebwa, Edridah, Kizza, Moses, and Elliott, Alison

Published
2018
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23. Parasitic, bacterial, viral, immune-mediated, metabolic and nutritional factors associated with nodding syndrome.

Author

Edridge, Arthur W. D., Abd-Elfarag, Gasim, Deijs, Martin, Broeks, Melissa H., Cristella, Cosimo, Sie, Brandon, Vaz, Frédéric M., Jans, Judith J. M., Calis, Job, Verhoef, Hans, Demir, Ayse, Poppert, Sven, Nickel, Beatrice, van Dam, Alje, Sebit, Boy, Titulaer, Maarten J., Verweij, Jaco J., de Jong, Menno D., van Gool, Tom, and Faragher, Brian

Published
2023
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24. SARS-CoV-2 Alpha-Variant Outbreak Amongst a Partially Vaccinated Long-Term Care Facility Population in The Netherlands—Phylogenetic Analysis and Infection Control Observations

Author

Van der Moeren, Nathalie, primary, Weterings, Veronica A. T. C., additional, Pas, Suzan D., additional, Verweij, Jaco J., additional, van den Bijllaardt, Wouter, additional, Geurts, Joyce, additional, Zwart, Vivian F., additional, Lodder, Esther B., additional, Kluytmans, Jan A. J. W., additional, Murk, Jean-Luc, additional, and Stohr, Joep J. J. M., additional

Published
2022
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27. Protection against malaria after immunization by chloroquine prophylaxis and sporozoites is mediated by preerythrocytic immunity

Author

Bijker, Else M., Bastiaens, Guido J. H., Teirlinck, Anne C., van Gemert, Geert-Jan, Graumans, Wouter, van de Vegte-Bolmer, Marga, Siebelink-Stoter, Rianne, Arens, Theo, Teelen, Karina, Nahrendorf, Wiebke, Remarque, Edmond J., Roeffen, Will, Jansens, Annemieke, Zimmerman, Dunja, Vos, Martijn, van Schaijk, Ben C. L., Wiersma, Jorien, van der Ven, André J. A. M., de Mast, Quirijn, van Lieshout, Lisette, Verweij, Jaco J., Hermsen, Cornelus C., Scholzen, Anja, and Sauerwein, Robert W.

Published
2013

28. SARS-CoV-2 Alpha-Variant Outbreak Amongst a Partially Vaccinated Long-Term Care Facility Population in The Netherlands—Phylogenetic Analysis and Infection Control Observations

Author

MMB Staf diagnostiek, Medische Microbiologie, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, MMB Medische Staf, Van der Moeren, Nathalie, Weterings, Veronica A.T.C., Pas, Suzan D., Verweij, Jaco J., van den Bijllaardt, Wouter, Geurts, Joyce, Zwart, Vivian F., Lodder, Esther B., Kluytmans, Jan A.J.W., Murk, Jean Luc, Stohr, Joep J.J.M., MMB Staf diagnostiek, Medische Microbiologie, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, MMB Medische Staf, Van der Moeren, Nathalie, Weterings, Veronica A.T.C., Pas, Suzan D., Verweij, Jaco J., van den Bijllaardt, Wouter, Geurts, Joyce, Zwart, Vivian F., Lodder, Esther B., Kluytmans, Jan A.J.W., Murk, Jean Luc, and Stohr, Joep J.J.M.

Published
2022

29. Self-testing for the detection of SARS-CoV-2 infection with rapid antigen tests for people with suspected COVID-19 in the community

Author

Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, Medische Microbiologie, Stohr, Joep J.J.M., Zwart, Vivian F., Goderski, Gabriel, Meijer, Adam, Nagel-Imming, Carla R.S., Kluytmans-van den Bergh, Marjolein F.Q., Pas, Suzan D., van den Oetelaar, Femke, Hellwich, Marloes, Gan, Kim H., Rietveld, Ariene, Verweij, Jaco J., Murk, Jean Luc, van den Bijllaardt, Wouter, Kluytmans, Jan A.J.W., Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, Medische Microbiologie, Stohr, Joep J.J.M., Zwart, Vivian F., Goderski, Gabriel, Meijer, Adam, Nagel-Imming, Carla R.S., Kluytmans-van den Bergh, Marjolein F.Q., Pas, Suzan D., van den Oetelaar, Femke, Hellwich, Marloes, Gan, Kim H., Rietveld, Ariene, Verweij, Jaco J., Murk, Jean Luc, van den Bijllaardt, Wouter, and Kluytmans, Jan A.J.W.

Published
2022

31. Assessment of environmental contamination with soil-transmitted helminths life stages at school compounds, households and open markets in Jimma Town, Ethiopia

Author

Tadege, Bamlaku, primary, Mekonnen, Zeleke, additional, Dana, Daniel, additional, Sharew, Bizuwarek, additional, Dereje, Eden, additional, Loha, Eskindir, additional, Verweij, Jaco J., additional, Casaert, Stijn, additional, Vlaminck, Johnny, additional, Ayana, Mio, additional, and Levecke, Bruno, additional

Published
2022
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32. Surveillance of leishmaniasis cases from 15 European centres, 2014 to 2019: a retrospective analysis

Author

Van der Auwera, Gert, Davidsson, Leigh, Buffet, Pierre, Ruf, Marie-Thérèse, Gramiccia, Marina, Varani, Stefania, Chicharro, Carmen, Bart, Aldert, Harms, Gundel, Chiodini, Peter L, Brekke, Hanne, Robert-Gangneux, Florence, Cortes, Sofia, Verweij, Jaco J, Scarabello, Alessandra, Karlsson Söbirk, Sara, Guéry, Romain, van Henten, Saskia, Di Muccio, Trentina, Carra, Elena, van Thiel, Pieter, Vandeputte, Martin, Gaspari, Valeria, Blum, Johannes, LeishMan Surveillance network, Van der Auwera G., Davidsson L., Buffet P., Ruf M.-T., Gramiccia M., Varani S., Chicharro C., Bart A., Harms G., Chiodini P.L., Brekke H., Robert-Gangneux F., Cortes S., Verweij J.J., Scarabello A., Karlsson Sobirk S., Guery R., van Henten S., Di Muccio T., Carra E., van Thiel P., Vandeputte M., Gaspari V., Blum J., APH - Global Health, Infectious diseases, AII - Infectious diseases, Chard-Hutchinson, Xavier, Institute of Tropical Medicine [Antwerp] (ITM), Public Health Agency of Sweden, CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University of Basel (Unibas), Istituto Superiore di Sanita [Rome], Azienda Ospedaliero Universitaria A. Meyer [Firenze, Italy], Instituto de Salud Carlos III [Madrid] (ISC), Amsterdam UMC - Amsterdam University Medical Center, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], University College London Hospitals (UCLH), Oslo University Hospital [Oslo], Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), École des Hautes Études en Santé Publique [EHESP] (EHESP), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), National Institute for Infectious Diseases 'Lazzaro Spallanzani', Lund University [Lund], Hôpital privé du Confluent [Nantes], Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna 'Bruno Ubertini' (IZSLER), and Istituto Superiore di Sanità (ISS)

Subjects
Adult, Male, Adolescent, Epidemiology, [SDV]Life Sciences [q-bio], Leishmaniasis, Cutaneous, imported, authochthonou, Young Adult, Virology, Humans, Authochthonous, Child, Leishmaniasis, leishmaniasis, travel, Aged, Retrospective Studies, Aged, 80 and over, Leishmania, Travel, Surveillance, Public Health, Environmental and Occupational Health, Infant, Newborn, Infant, Middle Aged, leishmaniasi, [SDV] Life Sciences [q-bio], Europe, Imported, Child, Preschool, surveillance, Leishmaniasis, Visceral, Female, authochthonous
Abstract

Background Surveillance of human leishmaniasis in Europe is mostly limited to country-specific information from autochthonous infections in the southern part. As at the end of 2021, no integrated analysis has been performed for cases seen across centres in different European countries. Aim To provide a broad perspective on autochthonous and imported leishmaniasis cases in endemic and non-endemic countries in Europe. Methods We retrospectively collected records from cutaneous, mucosal and visceral leishmaniasis cases diagnosed in 15 centres between 2014 and 2019. Centres were located in 11 countries: Belgium, France, Germany, Italy, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom. Data on country of infection, reason for travelling, infecting species, age and sex were analysed. Results We obtained diagnostic files from 1,142 cases, of which 76%, 21% and 3% had cutaneous, visceral, and mucosal disease, respectively. Of these, 68% were men, and 32% women, with the median age of 37 years (range: 0–90) at diagnosis. Visceral leishmaniasis was mainly acquired in Europe (88%; 167/190), while cutaneous leishmaniasis was primarily imported from outside Europe (77%; 575/749). Sixty-two percent of cutaneous leishmaniasis cases from outside Europe were from the Old World, and 38% from the New World. Geographic species distribution largely confirmed known epidemiology, with notable exceptions. Conclusions Our study confirms previous reports regarding geographic origin, species, and traveller subgroups importing leishmaniasis into Europe. We demonstrate the importance of pooling species typing data from many centres, even from areas where the aetiology is presumably known, to monitor changing epidemiology.

Published
2022

33. Re-emergence of enterovirus D68 in Europe after easing the COVID-19 lockdown, September 2021

Author

Benschop, Kimberley Sm, Albert, Jan, Anton, Andres, Andrés, Cristina, Aranzamendi, Maitane, Armannsdóttir, Brynja, Bailly, Jean-Luc, Baldanti, Fausto, Baldvinsdóttir, Guðrún Erna, Beard, Stuart, Berginc, Natasa, Böttcher, Sindy, Blomqvist, Soile, Bubba, Laura, Calvo, Cristina, Cabrerizo, Maria, Cavallero, Annalisa, Celma, Cristina, Ceriotti, Ferruccio, Costa, Inês, Cottrell, Simon, Del Cuerpo, Margarita, Dean, Jonathan, Dembinski, Jennifer L., Diedrich, Sabine, Diez-Domingo, Javier, Dorenberg, Dagnyhaug, Duizer, Erwin, Dyrdak, Robert, Fanti, Diana, Farkas, Agnes, Feeney, Susan, Flipse, Jacky, Gascun, Cillian, Galli, Cristina, Georgieva, Irina, Gifford, Laura, Guiomar, Raquel, Hönemann, Mario, Ikonen, Niina, Jeannoël, Marion, Josset, Laurence, Keeren, Kathrin, López-Labrador, F. Xavier, Maier, Melanie, Mckenna, James, Meijer, Adam, Mengual-Chuliá, Beatriz, Midgley, Sofie E., Mirand, Audrey, Montes, Milagrosa, Moore, Catherine, Morley, Ursula, Murk, Jean-Luc, Nikolaeva-Glomb, Lubomira, Numanovic, Sanela, Oggioni, Massimo, Palminha, Paula, Pariani, Elena, Pellegrinelli, Laura, Piralla, Antonio, Pietsch, Corinna, Piñeiro, Luis, Rabella, Núria, Rainetova, Petra, Sara Colonia UCEDA RENTERIA, Romero, María P., Reynders, Marijke, Roorda, Lieuwe, Savolainen-Kopra, Carita, Schuffenecker, Isabelle, Soynova, Aysa, Swanink, Caroline Ma, Ursic, Tina, Verweij, Jaco J., Vila, Jorgina, Vuorinen, Tytti, Simmonds, Peter, Fischer, Thea K., and Harvala, Heli

Subjects
enterovirus, respiratory infection, surveillance, typing, acute flaccid myelitis, enterovirus D68
Published
2021

36. Re-emergence of enterovirus D68 in Europe after easing the COVID-19 lockdown, September 2021

Author

Benschop, Kimberley SM, primary, Albert, Jan, additional, Anton, Andres, additional, Andrés, Cristina, additional, Aranzamendi, Maitane, additional, Armannsdóttir, Brynja, additional, Bailly, Jean-Luc, additional, Baldanti, Fausto, additional, Baldvinsdóttir, Guðrún Erna, additional, Beard, Stuart, additional, Berginc, Natasa, additional, Böttcher, Sindy, additional, Blomqvist, Soile, additional, Bubba, Laura, additional, Calvo, Cristina, additional, Cabrerizo, Maria, additional, Cavallero, Annalisa, additional, Celma, Cristina, additional, Ceriotti, Ferruccio, additional, Costa, Inês, additional, Cottrell, Simon, additional, del Cuerpo, Margarita, additional, Dean, Jonathan, additional, Dembinski, Jennifer L, additional, Diedrich, Sabine, additional, Diez-Domingo, Javier, additional, Dorenberg, DagnyHaug, additional, Duizer, Erwin, additional, Dyrdak, Robert, additional, Fanti, Diana, additional, Farkas, Agnes, additional, Feeney, Susan, additional, Flipse, Jacky, additional, De Gascun, Cillian, additional, Galli, Cristina, additional, Georgieva, Irina, additional, Gifford, Laura, additional, Guiomar, Raquel, additional, Hönemann, Mario, additional, Ikonen, Niina, additional, Jeannoël, Marion, additional, Josset, Laurence, additional, Keeren, Kathrin, additional, López-Labrador, F Xavier, additional, Maier, Melanie, additional, McKenna, James, additional, Meijer, Adam, additional, Mengual-Chuliá, Beatriz, additional, Midgley, Sofie E, additional, Mirand, Audrey, additional, Montes, Milagrosa, additional, Moore, Catherine, additional, Morley, Ursula, additional, Murk, Jean-Luc, additional, Nikolaeva-Glomb, Lubomira, additional, Numanovic, Sanela, additional, Oggioni, Massimo, additional, Palminha, Paula, additional, Pariani, Elena, additional, Pellegrinelli, Laura, additional, Piralla, Antonio, additional, Pietsch, Corinna, additional, Piñeiro, Luis, additional, Rabella, Núria, additional, Rainetova, Petra, additional, Uceda Renteria, Sara Colonia, additional, Romero, María P, additional, Reynders, Marijke, additional, Roorda, Lieuwe, additional, Savolainen-Kopra, Carita, additional, Schuffenecker, Isabelle, additional, Soynova, Aysa, additional, Swanink, Caroline MA, additional, Ursic, Tina, additional, Verweij, Jaco J, additional, Vila, Jorgina, additional, Vuorinen, Tytti, additional, Simmonds, Peter, additional, Fischer, Thea K, additional, and Harvala, Heli, additional

Published
2021
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40. Molecular Epidemiology and Evolutionary Trajectory of Emerging Echovirus 30, Europe

Author

Benschop, Kimberley S.M., primary, Broberg, Eeva K., additional, Hodcroft, Emma, additional, Schmitz, Dennis, additional, Albert, Jan, additional, Baicus, Anda, additional, Bailly, Jean-Luc, additional, Baldvinsdottir, Gudrun, additional, Berginc, Natasa, additional, Blomqvist, Soile, additional, Böttcher, Sindy, additional, Brytting, Mia, additional, Bujaki, Erika, additional, Cabrerizo, Maria, additional, Celma, Cristina, additional, Cinek, Ondrej, additional, Claas, Eric C.J., additional, Cremer, Jeroen, additional, Dean, Jonathan, additional, Dembinski, Jennifer L., additional, Demchyshyna, Iryna, additional, Diedrich, Sabine, additional, Dudman, Susanne, additional, Dunning, Jake, additional, Dyrdak, Robert, additional, Emmanouil, Mary, additional, Farkas, Agnes, additional, De Gascun, Cillian, additional, Fournier, Guillaume, additional, Georgieva, Irina, additional, Gonzalez-Sanz, Ruben, additional, van Hooydonk-Elving, Jolanda, additional, Jääskeläinen, Anne J., additional, Jancauskaite, Ruta, additional, Keeren, Kathrin, additional, Fischer, Thea K., additional, Krokstad, Sidsel, additional, Nikolaeva–Glomb, Lubomira, additional, Novakova, Ludmila, additional, Midgley, Sofie E., additional, Mirand, Audrey, additional, Molenkamp, Richard, additional, Morley, Ursula, additional, Mossong, Joël, additional, Muralyte, Svajune, additional, Murk, Jean-Luc, additional, Nguyen, Trung, additional, Nordbø, Svein A., additional, Österback, Riikka, additional, Pas, Suzan, additional, Pellegrinelli, Laura, additional, Pogka, Vassiliki, additional, Prochazka, Birgit, additional, Rainetova, Petra, additional, Van Ranst, Marc, additional, Roorda, Lieuwe, additional, Schuffenecker, Isabelle, additional, Schuurman, Rob, additional, Stoyanova, Asya, additional, Templeton, Kate, additional, Verweij, Jaco J., additional, Voulgari-Kokota, Androniki, additional, Vuorinen, Tytti, additional, Wollants, Elke, additional, Wolthers, Katja C., additional, Zakikhany, Katherina, additional, Neher, Richard, additional, Harvala, Heli, additional, and Simmonds, Peter, additional

Published
2021
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41. Molecular epidemiology and evolutionary trajectory of emerging echovirus 30, Europe

Author

Benschop, Kimberley S.M., Broberg, Eeva K., Hodcroft, Emma, Schmitz, Dennis, Albert, Jan, Baicus, Anda, Bailly, Jean Luc, Baldvinsdottir, Gudrun, Berginc, Natasa, Blomqvist, Soile, Böttcher, Sindy, Brytting, Mia, Bujaki, Erika, Cabrerizo, Maria, Celma, Cristina, Cinek, Ondrej, Claas, Eric C.J., Cremer, Jeroen, Dean, Jonathan, Dembinski, Jennifer L., Demchyshyna, Iryna, Diedrich, Sabine, Dudman, Susanne, Dunning, Jake, Dyrdak, Robert, Emmanouil, Mary, Farkas, Agnes, de Gascun, Cillian, Fournier, Guillaume, Georgieva, Irina, Gonzalez-Sanz, Ruben, van Hooydonk-Elving, Jolanda, Jääskeläinen, Anne J., Jancauskaite, Ruta, Keeren, Kathrin, Fischer, Thea K., Krokstad, Sidsel, Nikolaeva-Glomb, Lubomira, Novakova, Ludmila, Midgley, Sofie E., Mirand, Audrey, Molenkamp, Richard, Morley, Ursula, Mossong, Joël, Muralyte, Svajune, Murk, Jean Luc, Nguyen, Trung, Nordbø, Svein A., Österback, Riikka, Pas, Suzan, Pellegrinelli, Laura, Pogka, Vassiliki, Prochazka, Birgit, Rainetova, Petra, van Ranst, Marc, Roorda, Lieuwe, Schuffenecker, Isabelle, Schuurman, Rob, Stoyanova, Asya, Templeton, Kate, Verweij, Jaco J., Voulgari-Kokota, Androniki, Vuorinen, Tytti, Wollants, Elke, Wolthers, Katja C., Zakikhany, Katherina, Neher, Richard, Harvala, Heli, Simmonds, Peter, Benschop, Kimberley S.M., Broberg, Eeva K., Hodcroft, Emma, Schmitz, Dennis, Albert, Jan, Baicus, Anda, Bailly, Jean Luc, Baldvinsdottir, Gudrun, Berginc, Natasa, Blomqvist, Soile, Böttcher, Sindy, Brytting, Mia, Bujaki, Erika, Cabrerizo, Maria, Celma, Cristina, Cinek, Ondrej, Claas, Eric C.J., Cremer, Jeroen, Dean, Jonathan, Dembinski, Jennifer L., Demchyshyna, Iryna, Diedrich, Sabine, Dudman, Susanne, Dunning, Jake, Dyrdak, Robert, Emmanouil, Mary, Farkas, Agnes, de Gascun, Cillian, Fournier, Guillaume, Georgieva, Irina, Gonzalez-Sanz, Ruben, van Hooydonk-Elving, Jolanda, Jääskeläinen, Anne J., Jancauskaite, Ruta, Keeren, Kathrin, Fischer, Thea K., Krokstad, Sidsel, Nikolaeva-Glomb, Lubomira, Novakova, Ludmila, Midgley, Sofie E., Mirand, Audrey, Molenkamp, Richard, Morley, Ursula, Mossong, Joël, Muralyte, Svajune, Murk, Jean Luc, Nguyen, Trung, Nordbø, Svein A., Österback, Riikka, Pas, Suzan, Pellegrinelli, Laura, Pogka, Vassiliki, Prochazka, Birgit, Rainetova, Petra, van Ranst, Marc, Roorda, Lieuwe, Schuffenecker, Isabelle, Schuurman, Rob, Stoyanova, Asya, Templeton, Kate, Verweij, Jaco J., Voulgari-Kokota, Androniki, Vuorinen, Tytti, Wollants, Elke, Wolthers, Katja C., Zakikhany, Katherina, Neher, Richard, Harvala, Heli, and Simmonds, Peter

Abstract

In 2018, an upsurge in echovirus 30 (E30) infections was reported in Europe. We conducted a large-scale epidemiologic and evolutionary study of 1,329 E30 strains collected in 22 countries in Europe during 2016-2018. Most E30 cases affected persons 0-4 years of age (29%) and 25-34 years of age (27%). Sequences were divided into 6 genetic clades (G1-G6). Most (53%) sequences belonged to G1, followed by G6 (23%), G2 (17%), G4 (4%), G3 (0.3%), and G5 (0.2%). Each clade encompassed unique individual recombinant forms; G1 and G4 displayed >2 unique recombinant forms. Rapid turnover of new clades and recombinant forms occurred over time. Clades G1 and G6 dominated in 2018, suggesting the E30 upsurge was caused by emergence of 2 distinct clades circulating in Europe. Investigation into the mechanisms behind the rapid turnover of E30 is crucial for clarifying the epidemiology and evolution of these enterovirus infections.

Published
2021

42. Genome-wide analysis in Escherichia coli unravels a high level of genetic homoplasy associated with cefotaxime resistance

Author

dLAB Biobank, Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, Coolen, Jordy P.M., den Drijver, Evert P.M., Verweij, Jaco J., Schildkraut, Jodie A., Neveling, Kornelia, Melchers, Willem J.G., Kolwijck, Eva, Wertheim, Heiman F.L., Kluytmans, Jan A.J.W., Huynen, Martijn A., dLAB Biobank, Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, Coolen, Jordy P.M., den Drijver, Evert P.M., Verweij, Jaco J., Schildkraut, Jodie A., Neveling, Kornelia, Melchers, Willem J.G., Kolwijck, Eva, Wertheim, Heiman F.L., Kluytmans, Jan A.J.W., and Huynen, Martijn A.

Published
2021

43. Validation and maintaining laboratory developed molecular tests compliant with ISO15189 for diagnosis of intestinal parasitic infections.

Author

Verweij, Jaco J.

Abstract

Although, in the past few decades molecular diagnostics of parasitic infections have been accepted as first-line diagnostics, laboratories tend to be reluctant of introducing nucleic acid based tests as they dread the validation of laboratory developed tests (LDTs) compliant with ISO1589. This paper describes how to set tailor-made performance characteristics for the validation of laboratory developed tests (LDTs) for the molecular diagnosis of intestinal parasitic infections complying with the ISO 15189 guidelines. Then, just as important, maintaining these tests by daily monitoring, external quality assessment schemes, and reassessment of the test set-up. Tailoring performance characteristics for the validation of LDTs defining criteria that make sense and actually leading to a process of continuous quality improvement in the day-to-day practice of a diagnostic laboratory. It is essential or even obligatory to modify these characteristics, skip, or to add additional characteristics based on personal or changing insights fitted for a specific setting. [ABSTRACT FROM AUTHOR]

Published
2022
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44. Genome-wide analysis in Escherichia coli unravels a high level of genetic homoplasy associated with cefotaxime resistance

Author

Coolen, Jordy P. M., primary, den Drijver, Evert P. M., additional, Verweij, Jaco J., additional, Schildkraut, Jodie A., additional, Neveling, Kornelia, additional, Melchers, Willem J. G., additional, Kolwijck, Eva, additional, Wertheim, Heiman F. L., additional, Kluytmans, Jan A. J. W., additional, and Huynen, Martijn A., additional

Published
2021
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48. Limited Genetic Diversity of blaCMY-2-Containing IncI1-pST12 Plasmids from Enterobacteriaceae of Human and Broiler Chicken Origin in The Netherlands

Author

Drijver, Evert P M den, Stohr, Joep J J M, Verweij, Jaco J, Verhulst, Carlo, Velkers, Francisca C, Stegeman, Arjan, Bergh, Marjolein F Q Kluytmans-van den, Kluytmans, Jan A J W, Group, I-Health Study, FAH GZ pluimvee, dFAH I&I, FAH veterinaire epidemiologie, dFAH AVR, FAH GZ pluimvee, dFAH I&I, FAH veterinaire epidemiologie, and dFAH AVR

Subjects
0301 basic medicine, Microbiology (medical), AmpC β-lactamase, 030106 microbiology, Single-nucleotide polymorphism, Biology, Microbiology, DNA sequencing, Article, 03 medical and health sciences, Plasmid, Virology, plasmid, AmpC ß-lactamases, Replicon, lcsh:QH301-705.5, Gene, Genetics, Genetic diversity, Contig, biology.organism_classification, Enterobacteriaceae, 030104 developmental biology, lcsh:Biology (General), Horizontal gene transfer, blaCMY-2, IncI1
Abstract

Distinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission. We compared IncI1-pST12 plasmids from both human and livestock origin and explored the degree of sequence similarity between plasmids from Enterobacteriaceae with different epidemiological links. Short-read sequence data of Enterobacteriaceae cultured from humans and broilers were screened for the presence of both a blaCMY-2 gene and an IncI1-pST12 replicon. Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid assembly, pairwise single nucleotide polymorphisms (SNP) were determined. The plasmids were annotated, and a pan-genome was constructed to compare genes variably present between the different plasmids. Nine Escherichia coli sequences of broiler origin, four Escherichia coli sequences and one Salmonella enterica sequence of human origin were selected for the current analysis. A circular contig with the IncI1-pST12 replicon and blaCMY-2 gene was extracted from the assembly graph of all fourteen isolates. Analysis of the IncI1-pST12 plasmids revealed a low number of SNP differences (range of 0-9 SNPs). The range of SNP differences overlapped in isolates with different epidemiological links. One-hundred and twelve from a total of 113 genes of the pan-genome were present in all plasmid constructs. NGS-analysis of blaCMY--2-containing IncI1-pST12 plasmids isolated from Enterobacteriaceae with different epidemiological links show a high degree of sequence similarity in terms of SNP differences and the number of shared genes. Therefore, statements on the horizontal transfer of these plasmids based on genetic identity should be made with caution.

Published
2020

49. Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands

Author

Oude Munnink, Bas B., Nieuwenhuijse, David F., Stein, Mart, O’Toole, Áine, Haverkate, Manon, Mollers, Madelief, Kamga, Sandra K., Schapendonk, Claudia, Pronk, Mark, Lexmond, Pascal, van der Linden, Anne, Bestebroer, Theo, Chestakova, Irina, Overmars, Ronald J., van Nieuwkoop, Stefan, Molenkamp, Richard, van der Eijk, Annemiek A., GeurtsvanKessel, Corine, Vennema, Harry, Meijer, Adam, Rambaut, Andrew, van Dissel, Jaap, Sikkema, Reina S., Timen, Aura, Koopmans, Marion, Oudehuis, G. J. A. P. M., Schinkel, Janke, Kluytmans, Jan, Kluytmans-van den Bergh, Marjolein, van den Bijllaardt, Wouter, Berntvelsen, Robbert G., van Rijen, Miranda M. L., Schneeberger, Peter, Pas, Suzan, Diederen, Bram M., Bergmans, Anneke M. C., van der Eijk, P. A. Verspui, Verweij, Jaco J., Buiting, Anton G. N., Streefkerk, Roel, Aldenkamp, A. P., de Man, P., Koelemal, J. G. M., Ong, D., Paltansing, S., Veassen, N., Sleven, Jacqueline, Bakker, Leendert, Brockhoff, Heinrich, Rietveld, Ariene, Slijkerman Megelink, Fred, Cohen Stuart, James, de Vries, Anne, van der Reijden, Wil, Ros, A., Lodder, Esther, Verspui-van der Eijk, Ellen, Huijskens, Inge, Kraan, E. M., van der Linden, M. P. M., Debast, S. B., Naiemi, N. Al, Kroes, A. C. M., Damen, Marjolein, Dinant, Sander, Lekkerkerk, Sybren, Pontesilli, Oscar, Smit, Pieter, van Tienen, Carla, Godschalk, P. C. R., van Pelt, Jorien, Ott, Alewijn, van der Weijden, Charlie, Wertheim, Heiman, Rahamat-Langendoen, Janette, Reimerink, Johan, Bodewes, Rogier, Duizer, Erwin, van der Veer, Bas, Reusken, Chantal, Lutgens, Suzanne, Hermans, Mirjam, Wever, P., Leenders, A., ter Waarbeek, Henriette, Hoebe, Christian, Medical Microbiology and Infection Prevention, AII - Infectious diseases, Virology, RS: CAPHRI - R4 - Health Inequities and Societal Participation, and Med Microbiol, Infect Dis & Infect Prev

Subjects
0301 basic medicine, medicine.medical_specialty, Molecular biology, Clinical Decision-Making, Pneumonia, Viral, Genome, Viral, medicine.disease_cause, Disease cluster, General Biochemistry, Genetics and Molecular Biology, Betacoronavirus, 03 medical and health sciences, 0302 clinical medicine, SDG 3 - Good Health and Well-being, Environmental health, Pandemic, Epidemiology, medicine, Humans, Author Correction, Pandemics, Netherlands, Coronavirus, Respiratory tract diseases, Whole Genome Sequencing, biology, SARS-CoV-2, Transmission (medicine), Public health, COVID-19, Outbreak, Genomics, General Medicine, biology.organism_classification, 3. Good health, 030104 developmental biology, Geography, ZIKA, 030220 oncology & carcinogenesis, VIRUS, Public Health, Coronavirus Infections
Abstract

In late December 2019, a cluster of cases of pneumonia of unknown etiology were reported linked to a market in Wuhan, China1. The causative agent was identified as the speciesSevere acute respiratory syndrome-related coronavirusand was named SARS-CoV-2 (ref. 2). By 16 April the virus had spread to 185 different countries, infected over 2,000,000 people and resulted in over 130,000 deaths3. In the Netherlands, the first case of SARS-CoV-2 was notified on 27 February. The outbreak started with several different introductory events from Italy, Austria, Germany and France followed by local amplification in, and later also outside, the south of the Netherlands. The combination of near to real-time whole-genome sequence analysis and epidemiology resulted in reliable assessments of the extent of SARS-CoV-2 transmission in the community, facilitating early decision-making to control local transmission of SARS-CoV-2 in the Netherlands. We demonstrate how these data were generated and analyzed, and how SARS-CoV-2 whole-genome sequencing, in combination with epidemiological data, was used to inform public health decision-making in the Netherlands. Metastava project.

Published
2020

50. Limited Genetic Diversity of blaCMY-2-Containing IncI1-pST12 Plasmids from Enterobacteriaceae of Human and Broiler Chicken Origin in The Netherlands

Author

FAH GZ pluimvee, dFAH I&I, FAH veterinaire epidemiologie, dFAH AVR, Drijver, Evert P M den, Stohr, Joep J J M, Verweij, Jaco J, Verhulst, Carlo, Velkers, Francisca C, Stegeman, Arjan, Bergh, Marjolein F Q Kluytmans-van den, Kluytmans, Jan A J W, Group, I-Health Study, FAH GZ pluimvee, dFAH I&I, FAH veterinaire epidemiologie, dFAH AVR, Drijver, Evert P M den, Stohr, Joep J J M, Verweij, Jaco J, Verhulst, Carlo, Velkers, Francisca C, Stegeman, Arjan, Bergh, Marjolein F Q Kluytmans-van den, Kluytmans, Jan A J W, and Group, I-Health Study

Published
2020

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