Search

Your search keyword '"MORAN-GILAD, J."' showing total 210 results
Start Over Author "MORAN-GILAD, J."
210 results on '"MORAN-GILAD, J."'

13. An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities.

Author

O'Sullivan, DM, Doyle, RM, Temisak, S, Redshaw, N, Whale, AS, Logan, G, Huang, J, Fischer, N, Amos, GCA, Preston, MD, Marchesi, JR, Wagner, J, Parkhill, J, Motro, Y, Denise, H, Finn, RD, Harris, KA, Kay, GL, O'Grady, J, Ransom-Jones, E, Wu, H, Laing, E, Studholme, DJ, Benavente, ED, Phelan, J, Clark, TG, Moran-Gilad, J, Huggett, JF, O'Sullivan, DM, Doyle, RM, Temisak, S, Redshaw, N, Whale, AS, Logan, G, Huang, J, Fischer, N, Amos, GCA, Preston, MD, Marchesi, JR, Wagner, J, Parkhill, J, Motro, Y, Denise, H, Finn, RD, Harris, KA, Kay, GL, O'Grady, J, Ransom-Jones, E, Wu, H, Laing, E, Studholme, DJ, Benavente, ED, Phelan, J, Clark, TG, Moran-Gilad, J, and Huggett, JF

Abstract

Despite the advent of whole genome metagenomics, targeted approaches (such as 16S rRNA gene amplicon sequencing) continue to be valuable for determining the microbial composition of samples. Amplicon microbiome sequencing can be performed on clinical samples from a normally sterile site to determine the aetiology of an infection (usually single pathogen identification) or samples from more complex niches such as human mucosa or environmental samples where multiple microorganisms need to be identified. The methodologies are frequently applied to determine both presence of micro-organisms and their quantity or relative abundance. There are a number of technical steps required to perform microbial community profiling, many of which may have appreciable precision and bias that impacts final results. In order for these methods to be applied with the greatest accuracy, comparative studies across different laboratories are warranted. In this study we explored the impact of the bioinformatic approaches taken in different laboratories on microbiome assessment using 16S rRNA gene amplicon sequencing results. Data were generated from two mock microbial community samples which were amplified using primer sets spanning five different variable regions of 16S rRNA genes. The PCR-sequencing analysis included three technical repeats of the process to determine the repeatability of their methods. Thirteen laboratories participated in the study, and each analysed the same FASTQ files using their choice of pipeline. This study captured the methods used and the resulting sequence annotation and relative abundance output from bioinformatic analyses. Results were compared to digital PCR assessment of the absolute abundance of each target representing each organism in the mock microbial community samples and also to analyses of shotgun metagenome sequence data. This ring trial demonstrates that the choice of bioinformatic analysis pipeline alone can result in different estimations of the c

Published
2021

14. Omics for forensic and post-mortem microbiology

Author

Moran-Gilad, Jacob, Yagel, Yael, Moran-Gilad, J ( Jacob ), Yagel, Y ( Yael ), Fernández-Rodríguez, Amparo, González-Candelas, Fernando, Arora, Natasha, Moran-Gilad, Jacob, Yagel, Yael, Moran-Gilad, J ( Jacob ), Yagel, Y ( Yael ), Fernández-Rodríguez, Amparo, González-Candelas, Fernando, and Arora, Natasha

Abstract

Forensic microbiology, is a relatively new scientific field, attempting to utilise our knowledge of the evolution and habitats of different microorganisms. The introduction of high-throughput sequencing (HTS) technologies to various applications in microbiology has the potential to promote the field of forensic microbiology making it a valuable tool in the evaluation of a crime scene. In this chapter, we will thoroughly review what is known on forensic microbiology in de-termining the cause of death (COD), the study of pathogen transmission between donor-recipient pairs, the source(s) of outbreaks, the identification of body fluids or the identification of individuals through the microbial composition of their remains, to name just a few of the current applications. We will also discuss the challenges and obstacles in introducing this novel technology into courtrooms. Although yet under development and not presented in court cases so far, within the last 2 years some groups have been trying to apply HTS techniques to the diagnosis of infection as a COD. These advances are summarised here.

Published
2021

16. P026 Microbial Diversity is affected by Cognitive Behavioral and Mindfulness-Based Stress Reduction and accompanied by an Inflammatory Response in Patients with Crohn’s Disease

Author

Ilan, K, primary, Motro, Y, additional, Nemirovsky, A, additional, Lerner, L, additional, Schwartz, D, additional, Goren, G, additional, Sergienko, R, additional, Greenberg, D, additional, Slonim-Nevo, V, additional, Sarid, O, additional, Friger, M, additional, Regev, S, additional, Odes, S, additional, Moran-Gilad, J, additional, and Monsonego, A, additional

Published
2021
Full Text
View/download PDF

17. Setting a baseline for global urban virome surveillance in sewage

Author

Nieuwenhuijse, D.F. (David F.), Oude Munnink, B.B. (Bas B.), Phan, M.V.T. (My V. T.), Hendriksen, R.S. (Rene S.), Bego, A. (Artan), Rees, C. (Catherine), Neilson, E.H. (Elizabeth Heather), Coventry, K. (Kris), Collignon, P. (Peter), Allerberger, F. (Franz), Rahube, T.O. (Teddie O.), Oliveira, G. (Guilherme), Ivanov, I. (Ivan), Sopheak, T. (Thet), Vuthy, Y. (Yith), Yost, C.K. (Christopher K.), Tabo, D.-A. (Djim-adjim), Cuadros-Orellana, S. (Sara), Ke, C. (Changwen), Zheng, H. (Huanying), Baisheng, L. (Li), Jiao, X. (Xiaoyang), Donado-Godoy, P. (Pilar), Coulibaly, K.J. (Kalpy Julien), Hrenovic, J. (Jasna), Jergović, M. (Matijana), Karpíšková, R. (Renáta), Elsborg, B. (Bodil), Legesse, M. (Mengistu), Eguale, T. (Tadesse), Heikinheimo, A. (Annamari), Villacis, J.E. (Jose Eduardo), Sanneh, B. (Bakary), Malania, L. (Lile), Nitsche, A., Brinkmann, A. (Annika), Saba, C.K.S. (Courage Kosi Setsoafia), Kocsis, B. (Bela), Solymosi, N. (Norbert), Thorsteinsdottir, T.R. (Thorunn R.), Hatha, A.M. (Abdulla Mohamed), Alebouyeh, M. (Masoud), Morris, D. (Douglas), O’Connor, L. (Louise), Cormican, M. (M.), Moran-Gilad, J. (Jacob), Battisti, A. (Antonio), Alba, P. (Patricia), Shakenova, Z. (Zeinegul), Kiiyukia, C. (Ciira), Ng’eno, E. (Eric), Raka, L. (Lul), Bērziņš, A. (Aivars), Avsejenko, J. (Jeļena), Bartkevics, V. (Vadims), Penny, C. (Christian), Rajandas, H. (Heraa), Parimannan, S. (Sivachandran), Haber, M.V. (Malcolm Vella), Pal, P. (Pushkar), Schmitt, H. (Heike), van Passel, M. (Mark), van de Schans, M.G.M. (Milou G.M.), Zuidema, T. (Tina), Jeunen, G.-J. (Gert-Jan), Gemmell, N. (Neil), Fashae, K. (Kayode), Wester, A.L. (Astrid Louise), Holmstad, R. (Rune), Hasan, R. (Rumina), Shakoor, S. (Sadia), Rojas, M.L.Z. (Maria Luz Zamudio), Wasyl, D. (Dariusz), Bosevska, G. (Golubinka), Kochubovski, M. (Mihail), Radu, C. (Cojocaru), Gassama†, A. (Amy), Radosavljevic, V. (Vladimir), Tay, M.Y.F. (Moon Y.F.), Zuniga-Montanez, R. (Rogelio), Wuertz, S. (Stefan), Gavačová, D. (Dagmar), Trkov, M. (Marija), Keddy, K. (Karen), Esterhuyse, K. (Kerneels), Cerdà-Cuéllar, M. (Marta), Pathirage, S. (Sujatha), Larsson, D.G.J. (D.G.Joakim), Norrgren, L. (Leif), Örn, S. (Stefan), Van der Heijden, T. (Tanja), Kumburu, H.H. (Happiness Houka), de RodaHusman, A.M. (Ana Maria), Njanpop-Lafourcade, B.-M. (Berthe-Marie), Bidjada, P. (Pawou), Nikiema-Pessinaba, S.C. (Somtinda Christelle), Levent, B. (Belkis), Meschke, J.S. (John Scott), Beck, N.K. (Nicola Koren), Van Dang, C. (Chinh), Tran, D.M.N. (Doan Minh Nguyen), Do Phuc, N. (Nguyen), Kwenda, G. (Geoffrey), Munk, P. (Patrick), Venkatakrishnan, S. (Shweta), Aarestrup, F.M. (Frank), Cotten, M. (Matthew), Koopmans D.V.M., M.P.G. (Marion), Nieuwenhuijse, D.F. (David F.), Oude Munnink, B.B. (Bas B.), Phan, M.V.T. (My V. T.), Hendriksen, R.S. (Rene S.), Bego, A. (Artan), Rees, C. (Catherine), Neilson, E.H. (Elizabeth Heather), Coventry, K. (Kris), Collignon, P. (Peter), Allerberger, F. (Franz), Rahube, T.O. (Teddie O.), Oliveira, G. (Guilherme), Ivanov, I. (Ivan), Sopheak, T. (Thet), Vuthy, Y. (Yith), Yost, C.K. (Christopher K.), Tabo, D.-A. (Djim-adjim), Cuadros-Orellana, S. (Sara), Ke, C. (Changwen), Zheng, H. (Huanying), Baisheng, L. (Li), Jiao, X. (Xiaoyang), Donado-Godoy, P. (Pilar), Coulibaly, K.J. (Kalpy Julien), Hrenovic, J. (Jasna), Jergović, M. (Matijana), Karpíšková, R. (Renáta), Elsborg, B. (Bodil), Legesse, M. (Mengistu), Eguale, T. (Tadesse), Heikinheimo, A. (Annamari), Villacis, J.E. (Jose Eduardo), Sanneh, B. (Bakary), Malania, L. (Lile), Nitsche, A., Brinkmann, A. (Annika), Saba, C.K.S. (Courage Kosi Setsoafia), Kocsis, B. (Bela), Solymosi, N. (Norbert), Thorsteinsdottir, T.R. (Thorunn R.), Hatha, A.M. (Abdulla Mohamed), Alebouyeh, M. (Masoud), Morris, D. (Douglas), O’Connor, L. (Louise), Cormican, M. (M.), Moran-Gilad, J. (Jacob), Battisti, A. (Antonio), Alba, P. (Patricia), Shakenova, Z. (Zeinegul), Kiiyukia, C. (Ciira), Ng’eno, E. (Eric), Raka, L. (Lul), Bērziņš, A. (Aivars), Avsejenko, J. (Jeļena), Bartkevics, V. (Vadims), Penny, C. (Christian), Rajandas, H. (Heraa), Parimannan, S. (Sivachandran), Haber, M.V. (Malcolm Vella), Pal, P. (Pushkar), Schmitt, H. (Heike), van Passel, M. (Mark), van de Schans, M.G.M. (Milou G.M.), Zuidema, T. (Tina), Jeunen, G.-J. (Gert-Jan), Gemmell, N. (Neil), Fashae, K. (Kayode), Wester, A.L. (Astrid Louise), Holmstad, R. (Rune), Hasan, R. (Rumina), Shakoor, S. (Sadia), Rojas, M.L.Z. (Maria Luz Zamudio), Wasyl, D. (Dariusz), Bosevska, G. (Golubinka), Kochubovski, M. (Mihail), Radu, C. (Cojocaru), Gassama†, A. (Amy), Radosavljevic, V. (Vladimir), Tay, M.Y.F. (Moon Y.F.), Zuniga-Montanez, R. (Rogelio), Wuertz, S. (Stefan), Gavačová, D. (Dagmar), Trkov, M. (Marija), Keddy, K. (Karen), Esterhuyse, K. (Kerneels), Cerdà-Cuéllar, M. (Marta), Pathirage, S. (Sujatha), Larsson, D.G.J. (D.G.Joakim), Norrgren, L. (Leif), Örn, S. (Stefan), Van der Heijden, T. (Tanja), Kumburu, H.H. (Happiness Houka), de RodaHusman, A.M. (Ana Maria), Njanpop-Lafourcade, B.-M. (Berthe-Marie), Bidjada, P. (Pawou), Nikiema-Pessinaba, S.C. (Somtinda Christelle), Levent, B. (Belkis), Meschke, J.S. (John Scott), Beck, N.K. (Nicola Koren), Van Dang, C. (Chinh), Tran, D.M.N. (Doan Minh Nguyen), Do Phuc, N. (Nguyen), Kwenda, G. (Geoffrey), Munk, P. (Patrick), Venkatakrishnan, S. (Shweta), Aarestrup, F.M. (Frank), Cotten, M. (Matthew), and Koopmans D.V.M., M.P.G. (Marion)

Abstract

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.

Published
2020
Full Text
View/download PDF

18. Setting a baseline for global urban virome surveillance in sewage

Author

Nieuwenhuijse, D.F., Oude Munnink, B.B., Phan, M.V.T., Hendriksen, R.S., Bego, A., Rees, C., Neilson, E.H., Coventry, K., Collignon, P., Allerberger, F., Rahube, T.O., Oliveira, G., Ivanov, I., Sopheak, T., Vuthy, Y., Yost, C.K., Tabo, D.-A., Cuadros-Orellana, S., Ke, C., Zheng, H., Baisheng, L., Jiao, X., Donado-Godoy, P., Coulibaly, K.J., Hrenovic, J., Jergović, M., Karpíšková, R., Elsborg, B., Legesse, M., Eguale, T., Heikinheimo, A., Villacis, J.E., Sanneh, B., Malania, L., Nitsche, A., Brinkmann, A., Saba, C.K.S., Kocsis, B., Solymosi, N., Thorsteinsdottir, T.R., Hatha, A.M., Alebouyeh, M., Morris, D., O’Connor, L., Cormican, M., Moran-Gilad, J., Battisti, A., Alba, P., Shakenova, Z., Kiiyukia, C., Ng’eno, E., Raka, L., Bērziņš, A., Avsejenko, J., Bartkevics, V., Penny, C., Rajandas, H., Parimannan, S., Haber, M.V., Pal, P., Schmitt, H., van Passel, M., van de Schans, M.G.M., Zuidema, T., Jeunen, G.-J., Gemmell, N., Fashae, K., Wester, A.L., Holmstad, R., Hasan, R., Shakoor, S., Rojas, M.L.Z., Wasyl, D., Bosevska, G., Kochubovski, M., Radu, C., Gassama†, A., Radosavljević, Vladimir, Tay, M.Y.F., Zuniga-Montanez, R., Wuertz, S., Gavačová, D., Trkov, M., Keddy, K., Esterhuyse, K., Cerdà-Cuéllar, M., Pathirage, S., Larsson, D.G.J., Norrgren, L., Örn, S., Van der Heijden, T., Kumburu, H.H., de RodaHusman, A.M., Njanpop-Lafourcade, B.-M., Bidjada, P., Nikiema-Pessinaba, S.C., Levent, B., Meschke, J.S., Beck, N.K., Van Dang, C., Tran, D.M.N., Do Phuc, N., Kwenda, G., Munk, P., Venkatakrishnan, S., Aarestrup, F.M., Cotten, M., Koopmans, M.P.G., Nieuwenhuijse, D.F., Oude Munnink, B.B., Phan, M.V.T., Hendriksen, R.S., Bego, A., Rees, C., Neilson, E.H., Coventry, K., Collignon, P., Allerberger, F., Rahube, T.O., Oliveira, G., Ivanov, I., Sopheak, T., Vuthy, Y., Yost, C.K., Tabo, D.-A., Cuadros-Orellana, S., Ke, C., Zheng, H., Baisheng, L., Jiao, X., Donado-Godoy, P., Coulibaly, K.J., Hrenovic, J., Jergović, M., Karpíšková, R., Elsborg, B., Legesse, M., Eguale, T., Heikinheimo, A., Villacis, J.E., Sanneh, B., Malania, L., Nitsche, A., Brinkmann, A., Saba, C.K.S., Kocsis, B., Solymosi, N., Thorsteinsdottir, T.R., Hatha, A.M., Alebouyeh, M., Morris, D., O’Connor, L., Cormican, M., Moran-Gilad, J., Battisti, A., Alba, P., Shakenova, Z., Kiiyukia, C., Ng’eno, E., Raka, L., Bērziņš, A., Avsejenko, J., Bartkevics, V., Penny, C., Rajandas, H., Parimannan, S., Haber, M.V., Pal, P., Schmitt, H., van Passel, M., van de Schans, M.G.M., Zuidema, T., Jeunen, G.-J., Gemmell, N., Fashae, K., Wester, A.L., Holmstad, R., Hasan, R., Shakoor, S., Rojas, M.L.Z., Wasyl, D., Bosevska, G., Kochubovski, M., Radu, C., Gassama†, A., Radosavljević, Vladimir, Tay, M.Y.F., Zuniga-Montanez, R., Wuertz, S., Gavačová, D., Trkov, M., Keddy, K., Esterhuyse, K., Cerdà-Cuéllar, M., Pathirage, S., Larsson, D.G.J., Norrgren, L., Örn, S., Van der Heijden, T., Kumburu, H.H., de RodaHusman, A.M., Njanpop-Lafourcade, B.-M., Bidjada, P., Nikiema-Pessinaba, S.C., Levent, B., Meschke, J.S., Beck, N.K., Van Dang, C., Tran, D.M.N., Do Phuc, N., Kwenda, G., Munk, P., Venkatakrishnan, S., Aarestrup, F.M., Cotten, M., and Koopmans, M.P.G.

Abstract

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.

Published
2020

20. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Author

Hendriksen, R.S., Munk, P., Njage, P., van Bunnik, B., McNally, L., Lukjancenko, O., Röder, T., Nieuwenhuijse, D., Pedersen, S.K., Kjeldgaard, J., Kaas, R.S., Clausen, P.T.L.C., Vogt, J.K., Leekitcharoenphon, P., van de Schans, M.G.M., Zuidema, T., de Roda Husman, A.M., Rasmussen, S., Petersen, B., Bego, A., Rees, C., Cassar, S., Coventry, K., Collignon, P., Allerberger, F., Rahube, T.O., Oliveira, G., Ivanov, I., Vuthy, Y., Sopheak, T., Yost, C.K., Ke, C., Zheng, H., Baisheng, L., Jiao, X., Donado-Godoy, P., Coulibaly, K.J., Jergović, M., Hrenovic, J., Karpíšková, R., Villacis, J.E., Legesse, M., Eguale, T., Heikinheimo, A., Malania, L., Nitsche, A., Brinkmann, A., Saba, C.K.S., Kocsis, B., Solymosi, N., Thorsteinsdottir, T.R., Hatha, A.M., Alebouyeh, M., Morris, D., Cormican, M., O’Connor, L., Moran-Gilad, J., Alba, P., Battisti, A., Shakenova, Z., Kiiyukia, C., Ng’eno, E., Raka, L., Avsejenko, J., Bērziņš, A., Bartkevics, V., Penny, C., Rajandas, H., Parimannan, S., Haber, M.V., Pal, P., Jeunen, G.-J., Gemmell, N., Fashae, K., Holmstad, R., Hasan, R., Shakoor, S., Rojas, M.L.Z., Wasyl, D., Bosevska, G., Kochubovski, M., Radu, C., Gassama, A., Radosavljevic, V., Wuertz, S., Zuniga-Montanez, R., Tay, M.Y.F., Gavačová, D., Pastuchova, K., Truska, P., Trkov, M., Esterhuyse, K., Keddy, K., Cerdà-Cuéllar, M., Pathirage, S., Norrgren, L., Örn, S., Larsson, D.G.J., Heijden, T.V., Kumburu, H.H., Sanneh, B., Bidjada, P., Njanpop-Lafourcade, B.-M., Nikiema-Pessinaba, S.C., Levent, B., Meschke, J.S., Beck, N.K., Van, C.D., Phuc, N.D., Tran, D.M.N., Kwenda, G., Tabo, D.-A., Wester, A.L., Cuadros-Orellana, S., Amid, C., Cochrane, G., Sicheritz-Ponten, T., Schmitt, H., Alvarez, J.R.M., Aidara-Kane, A., Pamp, S.J., Lund, O., Hald, T., Woolhouse, M., Koopmans, M.P., Vigre, H., Petersen, T.N., Aarestrup, F.M.

Subjects
Global surveillance, antimicrobial resistance, AMR, wastewater, sewage, metagenomics, resistome, machine learning, prediction
Abstract

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomics analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross- selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socioeconomic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.

Published
2019

21. The successful uptake and sustainability of rapid infectious disease and antimicrobial resistance point-of-care testing requires a complex 'mix-and-match' implementation package

Author

Hays, J.P. (John), Mitsakakis, K, Luz, S., Belkum, A.F. (Alex) van, Becker, K., Bruel, A. (Ann) van den, Harbarth, S. (Stephan), Rex, J.H., Simonsen, G.S., Werner, G., Di Gregori, V., Ludke, G., Staa, T.P. (Tjeerd) van, Moran-Gilad, J., Bachmann, T.T., Hays, J.P. (John), Mitsakakis, K, Luz, S., Belkum, A.F. (Alex) van, Becker, K., Bruel, A. (Ann) van den, Harbarth, S. (Stephan), Rex, J.H., Simonsen, G.S., Werner, G., Di Gregori, V., Ludke, G., Staa, T.P. (Tjeerd) van, Moran-Gilad, J., and Bachmann, T.T.

Abstract

The emergence and spread of antimicrobial resistance is one of the major global issues currently threatening the health and wealth of nations, with effective guidelines and intervention strategies urgently required. Such guidelines and interventions should ideally be targeted at individuals, communities, and nations, requiring international coordination for maximum effect. In this respect, the European Joint Programming Initiative on Antimicrobial Resistance Transnational Working Group ‘Antimicrobial Resistance - Rapid Diagnostic Tests’ (JPIAMR AMR-RDT) is proposing to consider a ‘mix-and-match’ package for the implementation of point-of-care testing (PoCT), which is described in this publication. The working group was established with the remit of identifying barriers and solutions to th

Published
2019
Full Text
View/download PDF

22. The successful uptake and sustainability of rapid infectious disease and antimicrobial resistance point-of-care testing requires a complex 'mix-and-match' implementation package

Author

Hays, John, Mitsakakis, K, Luz, S, Belkum, A, Becker, K, van den Bruel, A, Harbarth, S, Rex, JH, Simonsen, GS, Werner, G, Di Gregori, V, Ludke, G, van Staa, T, Moran-Gilad, J, Bachmann, TT, Hays, John, Mitsakakis, K, Luz, S, Belkum, A, Becker, K, van den Bruel, A, Harbarth, S, Rex, JH, Simonsen, GS, Werner, G, Di Gregori, V, Ludke, G, van Staa, T, Moran-Gilad, J, and Bachmann, TT

Published
2019

23. Developmental roadmap for antimicrobial susceptibility testing systems

Author

Belkum, A, Bachmann, TT, Ludke, G, Lisby, JG, Kahlmeter, G, Mohess, A, Becker, K, Hays, John, Woodford, N, Mitsakakis, K, Moran-Gilad, J, Vila, J, Peter, H, Rex, JH, Dunne, WM, Belkum, A, Bachmann, TT, Ludke, G, Lisby, JG, Kahlmeter, G, Mohess, A, Becker, K, Hays, John, Woodford, N, Mitsakakis, K, Moran-Gilad, J, Vila, J, Peter, H, Rex, JH, and Dunne, WM

Published
2019

24. A Primer On Microbial Bioinformatics For Nonbioinformaticians

Author

Carrico, J. A., Rossi, M., Moran-Gilad, J., Van Domselaar, G., and Ramirez, M.

Abstract

Background: Presently, the bottleneck in the deployment of high-throughput sequencing technology is the ability to analyse the increasing amount of data produced in a fit-for-purpose manner. The field of microbial bioinformatics is thriving and quickly adapting to technological changes, which creates difficulties for nonbioinformaticians in following the complexity and increasingly obscure jargon of this field.

Published
2018

27. Developmental roadmap for antimicrobial susceptibility testing systems

Author

Belkum, A.F. (Alex) van, Bachmann, T.T. (Till T.), Lüdke, G. (Gerd), Lisby, J.G. (Jan Gorm), Kahlmeter, G., Mohess, A. (Allan), Becker, K. (Karsten), Hays, J.P. (John), Woodford, N. (Neil), Mitsakakis, K. (Konstantinos), Moran-Gilad, J. (Jacob), Vila, J. (Jordi), Peter, H. (Harald), Rex, J.H. (John H.), Dunne, W.M. (William Michael), Belkum, A.F. (Alex) van, Bachmann, T.T. (Till T.), Lüdke, G. (Gerd), Lisby, J.G. (Jan Gorm), Kahlmeter, G., Mohess, A. (Allan), Becker, K. (Karsten), Hays, J.P. (John), Woodford, N. (Neil), Mitsakakis, K. (Konstantinos), Moran-Gilad, J. (Jacob), Vila, J. (Jordi), Peter, H. (Harald), Rex, J.H. (John H.), and Dunne, W.M. (William Michael)

Abstract

Antimicrobial susceptibility testing (AST) technologies help to accelerate the initiation of targeted antimicrobial therapy for patients with infections and could potentially extend the lifespan of current narrow-spectrum antimicrobials. Although conceptually new and rapid AST technologies have been described, including new phenotyping methods, digital imaging and genomic approaches, there is no single major, or broadly accepted, technological breakthrough that leads the field of rapid AST platform development. This might be owing to several barriers that prevent the timely development and implementation of novel and rapid AST platforms in health-care settings. In this Consensus Statement, we explore such barriers, which include the utility of new methods, the complex process of validating new technology against reference methods beyond the proof-of-concept phase, the legal and regulatory landscapes, costs, the uptake of new tools, reagent stability, optimization of target product profiles, difficulties conducting clinical trials and issues relating to quality and quality control, and present possible solutions.

Published
2018
Full Text
View/download PDF

30. Real-time genomic investigation underlying the public health response to a Shiga toxin-producingEscherichia coliO26:H11 outbreak in a nursery

Author

MORAN-GILAD, J., primary, ROKNEY, A., additional, DANINO, D., additional, FERDOUS, M., additional, ALSANA, F., additional, BAUM, M., additional, DUKHAN, L., additional, AGMON, V., additional, ANUKA, E., additional, VALINSKY, L., additional, YISHAY, R., additional, GROTTO, I., additional, ROSSEN, J. W. A., additional, and GDALEVICH, M., additional

Published
2017
Full Text
View/download PDF

32. Real-time genomic investigation underlying the public health response to a Shiga toxin-producing Escherichia coli O26:H11 outbreak in a nursery.

Author

MORAN-GILAD, J., ROKNEY, A., DANINO, D., FERDOUS, M., ALSANA, F., BAUM, M., DUKHAN, L., AGMON, V., ANUKA, E., VALINSKY, L., YISHAY, R., GROTTO, I., ROSSEN, J. W. A., and GDALEVICH, M.

Abstract

Shiga toxin-producing Escherichia coli (STEC) is a significant cause of gastrointestinal infection and the haemolytic-uremic syndrome (HUS). STEC outbreaks are commonly associated with food but animal contact is increasingly being implicated in its transmission. We report an outbreak of STEC affecting young infants at a nursery in a rural community (three HUS cases, one definite case, one probable case, three possible cases and five carriers, based on the combination of clinical, epidemiological and laboratory data) identified using culture-based and molecular techniques. The investigation identified repeated animal contact (animal farming and petting) as a likely source of STEC introduction followed by horizontal transmission. Whole genome sequencing (WGS) was used for real-time investigation of the incident and revealed a unique strain of STEC O26:H11 carrying stx2a and intimin. Following a public health intervention, no additional cases have occurred. This is the first STEC outbreak reported from Israel. WGS proved as a useful tool for rapid laboratory characterization and typing of the outbreak strain and informed the public health response at an early stage of this unusual outbreak. [ABSTRACT FROM AUTHOR]

Published
2017
Full Text
View/download PDF

33. Laboratory Challenges in Response to Silent Introduction and Sustained Transmission of Wild Poliovirus Type 1 in Israel During 2013

Author

Shulman, L. M., primary, Mendelson, E., additional, Anis, E., additional, Bassal, R., additional, Gdalevich, M., additional, Hindiyeh, M., additional, Kaliner, E., additional, Kopel, E., additional, Manor, Y., additional, Moran-Gilad, J., additional, Ram, D., additional, Sofer, D., additional, Somekh, E., additional, Tasher, D., additional, Weil, M., additional, Gamzu, R., additional, and Grotto, I., additional

Published
2014
Full Text
View/download PDF

37. Insidious reintroduction of wild poliovirus into Israel, 2013

Author

Anis, E, primary, Kopel, E, additional, Singer, S R, additional, Kaliner, E, additional, Moerman, L, additional, Moran-Gilad, J, additional, Sofer, D, additional, Manor, Y, additional, Shulman, L M, additional, Mendelson, E, additional, Gdalevich, M, additional, Lev, B, additional, Gamzu, R, additional, and Grotto, I, additional

Published
2013
Full Text
View/download PDF

40. Continued emergence and changing epidemiology of oseltamivir-resistant influenza A(H1N1)2009 virus, United Kingdom, winter 2010/11

Author

Lackenby, A, primary, Moran Gilad, J, additional, Pebody, R, additional, Miah, S, additional, Calatayud, L, additional, Bolotin, S, additional, Vipond, I, additional, Muir, P, additional, Guiver, M, additional, McMenamin, J, additional, Reynolds, A, additional, Moore, C, additional, Gunson, R, additional, Thompson, CI, additional, Galiano, M, additional, Bermingham, A, additional, Ellis, J, additional, and Zambon, M, additional

Published
2011
Full Text
View/download PDF

44. Humidifier-associated paediatric Legionnaires' disease, Israel, February 2012

Author

Moran-Gilad J, Lazarovitch T, Massimo Mentasti, Harrison T, Weinberger M, Mordish Y, Mor Z, Stocki T, Anis E, Sadik C, Amitai Z, and Grotto I

Subjects
Cold Temperature, Molecular Typing, Equipment Contamination, Humans, Infant, Humidity, Equipment Design, Israel, Legionnaires' Disease, Water Microbiology, Pediatrics, Legionella pneumophila
Abstract

We report a fatal case of community-acquired Legionnaires' disease in an infant aged under six months. Epidemiological and microbiological investigations suggested that a free-standing cold water humidifier using domestic tap water contaminated with Legionella pneumophila serogroup 1 served as a vehicle for infection. These findings were corroborated by sequence-based typing (SBT). Humidifier-associated Legionnaires' disease can be prevented by appropriate control measures. This case also illustrates the emerging role of SBT in the investigation of legionellosis.

45. Wildlife Pathogen Surveillance in Israel to Inform Human and Animal Infectious Disease Control: a Prioritization Exercise.

Author

Lapid, Roi, King, R., Yakobson, B., Shalom, U., and Moran-Gilad, J.

Subjects
*COMMUNICABLE diseases, *COMMUNICABLE diseases in animals, *HEALTH risk assessment, *FOOT & mouth disease, *BRUCELLOSIS in animals, *RABIES in animals, *PUBLIC health
Abstract

In December 2013, as a part of the establishment of the 'Israel Wildlife Diseases Surveillance'(IWDS) Program, building on the 'One Health' approach for human, livestock and wildlife disease control, a prioritization exercise using a validated risk analysis method was carried out by distributing online questionnaires to 86 relevant experts. The results were subsequently presented in the prioritization of a wildlife surveillance workshop, compiling the risk assessments of 51 pathogens by human, livestock, wildlife and total risks. The endemic diseases, brucellosis, rabies and foot and mouth disease ranked as the highest risks. The Risk Analysis method was used successfully in the prioritization exercise. Furthermore, the results combined surveillance priorities of relevant stakeholders and will be used in planning and implementing the national surveillance program. [ABSTRACT FROM AUTHOR]

Published
2016

46. The Epidemiology of PCR-Confirmed Cutaneous Leishmaniasis in Israel: A Nationwide Study.

Author

Avni D, Solomon M, Strauss M, Sagi O, Temper V, Michael-Gayego A, Meningher T, Avitan-Hersh E, Szwarcwort-Cohen M, Moran-Gilad J, Ollech A, and Schwartz E

Abstract

Background: Leishmaniasis, mainly cutaneous leishmaniasis (CL), is endemic in Israel. In recent years, the diagnosis of leishmaniasis has transitioned to a molecular diagnosis., Objective: To summarize all cases of leishmaniasis and the identified species seen in Israel based on molecular diagnosis., Methods: A retrospective study was performed of patients diagnosed with leishmaniasis between January 2017 and December 2022. All five medical centers in Israel in which Leishmania diagnosis is performed were included: Soroka, HaEmek, Hadassah, Rambam, and Sheba, all utilized molecular diagnostic methods. Data on the annual number of cases, species, age, and gender were retrieved., Results: During the years 2017-2022, a total of 4168 cases of leishmaniasis were diagnosed, which corresponds with ~7/100,000 inhabitants. L. (L.) major and L. (L.) tropica accounted for 84% and 14%, respectively. During the years 2020-2021, L. (L.) infantum emerged as a new form of cutaneous disease [2.7% of cases during this period]. Visceral L. (L.) infantum was found in five cases. Imported New World leishmaniasis accounted for 1% of the cases. L. (L.) major affected more males (67%) while L. (L.) tropica commonly affected more children and caused more facial lesions., Conclusions: The mean annual number of cases during these years is ~700. The dominant species is L. (L.) major. Since 2020, cutaneous L. (L.) infantum is an emerging infection in Israel.

Published
2024
Full Text
View/download PDF

47. Reduction in Serum Carotenoid Levels Following One Anastomosis Gastric Bypass.

Author

Harari A, Kaniel O, Keshet R, Shaish A, Kessler Y, Szold A, Langer P, Raziel A, Sakran N, Goitein D, Moran-Gilad J, and Sherf-Dagan S

Subjects
Humans, Female, Middle Aged, Male, Adult, Prospective Studies, Obesity, Morbid surgery, Obesity, Morbid blood, Weight Loss, Body Mass Index, Anastomosis, Surgical, Treatment Outcome, Gastric Bypass methods, Carotenoids blood
Abstract

Given the health benefits of carotenoids, it is crucial to evaluate their levels in patients undergoing malabsorptive procedures like one anastomosis gastric bypass (OAGB). This study aimed to assess serum carotenoid levels before and 6 months following OAGB. Prospectively collected data from patients who underwent primary OAGB were analyzed. Data included anthropometrics, dietary intake assessments, and biochemical tests. Serum samples were analyzed for lipid profile and serum carotenoids, including lutein, zeaxanthin, α-carotene, β-carotene, phytofluene, ζ-carotene, and lycopene. Data from 27 patients (median age 47.0 years and 55.6% female) were available before and 6 months post-OAGB. The median pre-surgical BMI was 39.5 kg/m 2 , and the median excess weight loss at 6 months post-surgery was 63.9%. Significant decreases in all carotenoid levels were observed over time ( p < 0.001 for all). A median relative decline of 65.1% in absolute total carotenoid levels and 12.7% in total cholesterol levels were found. No associations were observed between changes in clinical outcomes and carotenoid levels during the study period. This study reveals significant decreases in carotenoid levels within the first 6 months following OAGB. Nutritional intervention studies are needed to explore how incorporating carotenoid-rich foods affects post-surgery carotenoid levels and clinical outcomes.

Published
2024
Full Text
View/download PDF

48. In vivo selection of carbapenem resistance during persistent Klebsiella pneumoniae sequence type 395 bloodstream infection due to OmpK36 deletion.

Author

Strahilevitz J, Motro Y, Temper V, Merezhko D, Ayalon O, Bar Moshe Y, Lam MMC, Holt KE, and Moran-Gilad J

Subjects
Humans, Male, Bacteremia microbiology, Bacteremia drug therapy, Phylogeny, Genome, Bacterial genetics, Plasmids genetics, beta-Lactamases genetics, Klebsiella pneumoniae genetics, Klebsiella pneumoniae drug effects, Klebsiella pneumoniae isolation & purification, Klebsiella Infections drug therapy, Klebsiella Infections microbiology, Carbapenems pharmacology, Carbapenems therapeutic use, Porins genetics, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Bacterial Proteins genetics, Microbial Sensitivity Tests
Abstract

Non-carbapenemase-producing carbapenem-resistant Enterobacterales (non-CP CRE) may be associated with a grave outcome. The common underlying mechanism is beta-lactamases and mutations in outer membrane porins. We report a case of a deep-seated infection caused by Klebsiella pneumoniae ST395 not amenable to source control, involving recurrent bloodstream infection, resulting in in vivo selection of carbapenem resistance under therapy. Three consecutive K. pneumoniae blood isolates were studied using short- and long-read sequencing. The genomes were subject to resistome and virulome, phylogenetic, and plasmid analyses. ompK36 porins were analyzed at the nucleotide and amino acid levels. Genomes were compared to 297 public ST395 K. pneumoniae genomes using cgMLST, resistome, and porin analyses and the EuSCAPE project. Relevant ompK36 and micF sequences were extracted and analyzed as above. The three sequential K. pneumoniae blood isolates belonged to the same clone. Subsequent CR isolates revealed a new large deletion of the ompK36 gene also involving the upstream region (deletion of micF ). Comparison with public ST395 genomes revealed the study isolates belonged to clade B, representing a separate clone. N-terminal large ompK36 truncations were uncommon in both public data sets. In vivo selection of non-CP CRE K. pneumoniae could have substantial clinical implications. Such selection should be scrutinized through repeated cultures and frequent susceptibility testing during antimicrobial treatment, especially in the context of persistent or recurrent bloodstream infections and when adequate source control cannot be achieved. The occurrence of an unusually large deletion involving the ompK36 locus and upstream micF should be further studied., Competing Interests: The authors declare no conflict of interest.

Published
2024
Full Text
View/download PDF

49. Invasive infections caused by the recently described species Enterococcus innesii.

Author

Motro Y, Temper V, Strahilevitz J, and Moran-Gilad J

Subjects
Humans, Male, Whole Genome Sequencing, Genome, Bacterial, Aged, Female, Anti-Bacterial Agents therapeutic use, Anti-Bacterial Agents pharmacology, Middle Aged, Sepsis microbiology, Enterococcus genetics, Enterococcus classification, Enterococcus isolation & purification, Gram-Positive Bacterial Infections microbiology, Gram-Positive Bacterial Infections diagnosis
Abstract

E. innesii is a recently described Enterococcus species which may be difficult to differentiate from the more common E. casseliflavus. We present the first clinical report of invasive E. innesii infection, featuring two cases of biliary sepsis. Whole genome sequencing confirmed the taxonomic assignment and the presence of vanC-4. Analysis of public genomes identified 13 deposited E. innesii and 13 deposited E. casselifalvus/E.gallinarum genomes which could be reassigned as E. innesii. Improved laboratory diagnosis of E. innesii is expected to generate additional data concerning its clinical relevance and support the future diagnosis and treatment of this uncommon pathogen., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Published
2024
Full Text
View/download PDF

50. Ensuring accuracy in the development and application of nucleic acid amplification tests (NAATs) for infectious disease.

Author

Huggett JF, O'Sullivan DM, Cowen S, Cleveland MH, Davies K, Harris K, Moran-Gilad J, Winter A, Braybrook J, and Messenger M

Subjects
Humans, Pandemics, COVID-19 Nucleic Acid Testing methods, Sensitivity and Specificity, COVID-19 Testing methods, RNA, Viral genetics, Molecular Diagnostic Techniques methods, Molecular Diagnostic Techniques standards, Communicable Diseases diagnosis, Nucleic Acid Amplification Techniques methods, COVID-19 diagnosis, COVID-19 virology, COVID-19 epidemiology, SARS-CoV-2 genetics, SARS-CoV-2 isolation & purification
Abstract

Diagnostic tests were heralded as crucial during the Coronavirus disease (COVID-19) pandemic with most of the key methods using bioanalytical approaches that detected larger molecules (RNA, protein antigens or antibodies) rather than conventional clinical biochemical techniques. Nucleic Acid Amplification Tests (NAATs), like the Polymerase Chain Reaction (PCR), and other molecular methods, like sequencing (that often work in combination with NAATs), were essential to the diagnosis and management during COVID-19. This was exemplified both early in the pandemic but also later on, following the emergence of new genetic SARS-CoV-2 variants. The 100 day mission to respond to future pandemic threats highlights the need for effective diagnostics, therapeutics and vaccines. Of the three, diagnostics represents the first opportunity to manage infectious diseases while also being the most poorly supported in terms of the infrastructure needed to demonstrate effectiveness. Where performance targets exist, they are not well served by consensus on how to demonstrate they are being met; this includes analytical factors such as limit of detection (LOD) false positive results as well as how to approach clinical evaluation. The selection of gold standards or use of epidemiological factors such as predictive value, reference ranges or clinical thresholds are seldom correctly considered. The attention placed on molecular diagnostic tests during COVID-19 illustrates important considerations and assumptions on the use of these methods for infectious disease diagnosis and beyond. In this manuscript, we discuss state-of-the-art approaches to diagnostic evaluation and explore how they may be better tailored to diagnostic techniques like NAATs to maximise the impact of these highly versatile bioanalytical tools, both generally and during future outbreaks., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Published
2024
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results