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2. If Youre Not Confused, Youre Not Paying Attention: Ochrobactrum Is Not Brucella.

Author

Moreno, Edgardo, Middlebrook, Earl, Altamirano-Silva, Pamela, Al Dahouk, Sascha, Araj, George, Arce-Gorvel, Vilma, Arenas-Gamboa, Ángela, Ariza, Javier, Barquero-Calvo, Elías, Battelli, Giorgio, Bertu, Wilson, Blasco, José, Bosilkovski, Mile, Cadmus, Simeon, Caswell, Clayton, Celli, Jean, Chacón-Díaz, Carlos, Chaves-Olarte, Esteban, Comerci, Diego, Conde-Álvarez, Raquel, Cook, Elizabeth, Cravero, Silvio, Dadar, Maryam, De Boelle, Xavier, De Massis, Fabrizio, Díaz, Ramón, Escobar, Gabriela, Fernández-Lago, Luis, Ficht, Thomas, Foster, Jeffrey, Garin-Bastuji, Bruno, Godfroid, Jacques, Gorvel, Jean-Pierre, Güler, Leyla, Erdenliğ-Gürbilek, Sevil, Gusi, Amayel, Guzmán-Verri, Caterina, Hai, Jiang, Hernández-Mora, Gabriela, Iriarte, Maite, Jacob, Nestor, Keriel, Anne, Khames, Maamar, Köhler, Stephan, Letesson, Jean-Jacques, Loperena-Barber, Maite, López-Goñi, Ignacio, McGiven, John, Melzer, Falk, Mora-Cartin, Ricardo, Moran-Gilad, Jacob, Muñoz, Pilar, Neubauer, Heinrich, OCallaghan, David, Ocholi, Reuben, Oñate, Ángel, Pandey, Piyush, Pappas, Georgios, Pembroke, J, Roop, Martin, Ruiz-Villalonos, Nazaret, Ryan, Michael, Salcedo, Suzana, Salvador-Bescós, Miriam, Sangari, Félix, de Lima Santos, Renato, Seimenis, Aristarchos, Splitter, Gary, Suárez-Esquivel, Marcela, Tabbaa, Darem, Trangoni, Marcos, Vizcaíno, Nieves, Wareth, Gamal, Welburn, Susan, Whatmore, Adrian, Zúñiga-Ripa, Amaia, Moriyón, Ignacio, and Tsolis, Renée

Subjects
Brucella, Ochrobactrum, Ochrobactrum, Brucella, Terminology as Topic, Phylogeny, Brucellosis, Humans, Opportunistic Infections
Abstract

Bacteria of the genus Brucella are facultative intracellular parasites that cause brucellosis, a severe animal and human disease. Recently, a group of taxonomists merged the brucellae with the primarily free-living, phylogenetically related Ochrobactrum spp. in the genus Brucella. This change, founded only on global genomic analysis and the fortuitous isolation of some opportunistic Ochrobactrum spp. from medically compromised patients, has been automatically included in culture collections and databases. We argue that clinical and environmental microbiologists should not accept this nomenclature, and we advise against its use because (i) it was presented without in-depth phylogenetic analyses and did not consider alternative taxonomic solutions; (ii) it was launched without the input of experts in brucellosis or Ochrobactrum; (iii) it applies a non-consensus genus concept that disregards taxonomically relevant differences in structure, physiology, population structure, core-pangenome assemblies, genome structure, genomic traits, clinical features, treatment, prevention, diagnosis, genus description rules, and, above all, pathogenicity; and (iv) placing these two bacterial groups in the same genus creates risks for veterinarians, medical doctors, clinical laboratories, health authorities, and legislators who deal with brucellosis, a disease that is particularly relevant in low- and middle-income countries. Based on all this information, we urge microbiologists, bacterial collections, genomic databases, journals, and public health boards to keep the Brucella and Ochrobactrum genera separate to avoid further bewilderment and harm.

Published
2023

3. Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions

Author

Sollier, Julie, Basler, Marek, Broz, Petr, Dittrich, Petra S., Drescher, Knut, Egli, Adrian, Harms, Alexander, Hierlemann, Andreas, Hiller, Sebastian, King, Carolyn G., McKinney, John D., Moran-Gilad, Jacob, Neher, Richard A., Page, Malcolm G. P., Panke, Sven, Persat, Alexandre, Picotti, Paola, Rentsch, Katharina M., Rivera-Fuentes, Pablo, Sauer, Uwe, Stolz, Daiana, Tschudin-Sutter, Sarah, van Delden, Christian, van Nimwegen, Erik, Veening, Jan-Willem, Zampieri, Mattia, Zinkernagel, Annelies S., Khanna, Nina, Bumann, Dirk, Jenal, Urs, and Dehio, Christoph

Published
2024
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11. A framework for optimizing COVID-19 testing policy using a Multi Armed Bandit approach

Author

Grushka-Cohen, Hagit, Cohen, Raphael, Shapira, Bracha, Moran-Gilad, Jacob, and Rokach, Lior

Subjects
Computer Science - Machine Learning, Statistics - Machine Learning
Abstract

Testing is an important part of tackling the COVID-19 pandemic. Availability of testing is a bottleneck due to constrained resources and effective prioritization of individuals is necessary. Here, we discuss the impact of different prioritization policies on COVID-19 patient discovery and the ability of governments and health organizations to use the results for effective decision making. We suggest a framework for testing that balances the maximal discovery of positive individuals with the need for population-based surveillance aimed at understanding disease spread and characteristics. This framework draws from similar approaches to prioritization in the domain of cyber-security based on ranking individuals using a risk score and then reserving a portion of the capacity for random sampling. This approach is an application of Multi-Armed-Bandits maximizing exploration/exploitation of the underlying distribution. We find that individuals can be ranked for effective testing using a few simple features, and that ranking them using such models we can capture 65% (CI: 64.7%-68.3%) of the positive individuals using less than 20% of the testing capacity or 92.1% (CI: 91.1%-93.2%) of positives individuals using 70% of the capacity, allowing reserving a significant portion of the tests for population studies. Our approach allows experts and decision-makers to tailor the resulting policies as needed allowing transparency into the ranking policy and the ability to understand the disease spread in the population and react quickly and in an informed manner.

Published
2020

13. Quality of MALDI-TOF mass spectra in routine diagnostics: results from an international external quality assessment including 36 laboratories from 12 countries using 47 challenging bacterial strains

Author

Cuénod, Aline, Aerni, Martina, Bagutti, Claudia, Bayraktar, Banu, Boz, Efe Serkan, Carneiro, Cynthia Beisert, Casanova, Carlo, Coste, Alix T., Damborg, Peter, van Dam, Dirk W., Demirci, Mehmet, Drevinek, Pavel, Dubuis, Olivier, Fernandez, José, Greub, Gilbert, Hrabak, Jaroslav, Hürkal Yiğitler, Gülen, Hurych, Jakub, Jensen, Thøger Gorm, Jost, Géraldine, Kampinga, Greetje A., Kittl, Sonja, Lammens, Christine, Lang, Claudia, Lienhard, Reto, Logan, Julie, Maffioli, Carola, Mareković, Ivana, Marschal, Matthias, Moran-Gilad, Jacob, Nolte, Oliver, Oberle, Michael, Pedersen, Michael, Pflüger, Valentin, Pranghofer, Sigrid, Reichl, Julia, Rentenaar, Rob J., Riat, Arnaud, Rodríguez-Sánchez, Belén, Schilt, Camille, Schlotterbeck, Ann-Kathrin, Schrenzel, Jacques, Troib, Shani, Willems, Elise, Wootton, Mandy, Ziegler, Dominik, and Egli, Adrian

Published
2023
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16. The Epidemiology of PCR-Confirmed Cutaneous Leishmaniasis in Israel: A Nationwide Study.

Author

Avni, Dror, Solomon, Michal, Strauss, Merav, Sagi, Orli, Temper, Violeta, Michael-Gayego, Ayelet, Meningher, Tal, Avitan-Hersh, Emily, Szwarcwort-Cohen, Moran, Moran-Gilad, Jacob, Ollech, Ayelet, and Schwartz, Eli

Subjects
CUTANEOUS leishmaniasis, VISCERAL leishmaniasis, EMERGING infectious diseases, SKIN diseases, MOLECULAR diagnosis, LEISHMANIASIS
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. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Brucellosis Outbreak Traced to Commercially Sold Camel Milk through Whole-Genome Sequencing, Israel

Author

Bardenstein, Svetlana, Gibbs, Rachel E., Yagel, Yael, Motro, Yair, and Moran-Gilad, Jacob

Subjects
Nucleotide sequencing -- Usage, Epidemics -- Causes of -- Israel, Camels -- Health aspects, DNA sequencing -- Usage, Brucellosis -- Causes of, Milk contamination -- Health aspects, Health
Abstract

Brucellosis, caused by bacteria of the Brucella genus, is a neglected zoonotic disease that affects marginalized populations worldwide (1). Human transmission occurs mainly through consumption of unpasteurized, contaminated dairy products [...]

Published
2021
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22. Reduction in Serum Carotenoid Levels Following One Anastomosis Gastric Bypass.

Author

Harari, Ayelet, Kaniel, Osnat, Keshet, Rom, Shaish, Aviv, Kessler, Yafit, Szold, Amir, Langer, Peter, Raziel, Asnat, Sakran, Nasser, Goitein, David, Moran-Gilad, Jacob, and Sherf-Dagan, Shiri

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/m2, 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. [ABSTRACT FROM AUTHOR]

Published
2024
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23. Evaluation of an automated feedback intervention to improve antibiotic prescribing among primary care physicians (OPEN Stewardship): a multinational controlled interrupted time-series study

Author

Soucy, Jean-Paul R., primary, Low, Marcelo, additional, Acharya, Kamal R., additional, Ellen, Moriah, additional, Hulth, Anette, additional, Löfmark, Sonja, additional, Garber, Gary E., additional, Watson, William, additional, Moran-Gilad, Jacob, additional, Davidovitch, Nadav, additional, Amar, Tamar, additional, McCready, Janine, additional, Orava, Matthew, additional, Brownstein, John S., additional, Brown, Kevin A., additional, Fisman, David N., additional, and MacFadden, Derek R., additional

Published
2024
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24. In-depth characterization of multidrug-resistant NDM-1 and KPC-3 co-producing Klebsiella pneumoniae bloodstream isolates from Italian hospital patients

Author

Posteraro, Brunella, primary, De Maio, Flavio, additional, Motro, Yair, additional, Menchinelli, Giulia, additional, De Lorenzis, Desy, additional, Marano, Roberto B. M., additional, Aljanazreh, Bessan, additional, Errico, Federica Maria, additional, Massaria, Giuseppe, additional, Spanu, Teresa, additional, Posteraro, Patrizia, additional, Moran-Gilad, Jacob, additional, and Sanguinetti, Maurizio, additional

Published
2024
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25. An Evaluation of the Impact of an OPEN Stewardship Generated Feedback Intervention on Antibiotic Prescribing among Primary Care Veterinarians in Canada and Israel

Author

Acharya, Kamal R., primary, Cohen, Adar, additional, Brankston, Gabrielle, additional, Soucy, Jean-Paul R., additional, Hulth, Anette, additional, Löfmark, Sonja, additional, Brownstein, John S., additional, Davidovich, Nadav, additional, Ellen, Moriah E., additional, Fisman, David N., additional, Moran-Gilad, Jacob, additional, Steinman, Amir, additional, MacFadden, Derek R., additional, and Greer, Amy L., additional

Published
2024
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27. Expert guidance on target product profile development for AMR diagnostic tests

Author

Bachmann, Till T, primary, Mitsakakis, Konstantinos, additional, Hays, John P, additional, van Belkum, Alex, additional, Russom, Aman, additional, Luedke, Gerd, additional, Simonsen, Gunnar Skov, additional, Abel, Gyorgy, additional, Peter, Harald, additional, Goossens, Herman, additional, Moran-Gilad, Jacob, additional, Vila, Jordi, additional, Becker, Karsten, additional, Moons, Pieter, additional, Sampath, Rangarajan, additional, Peeling, Rosanna W, additional, Luz, Saturnino, additional, van Staa, Tjeerd, additional, and Di Gregori, Valentina, additional

Published
2023
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28. Rethinking wastewater risks and monitoring in light of the COVID-19 pandemic

Author

Bogler, Anne, Packman, Aaron, Furman, Alex, Gross, Amit, Kushmaro, Ariel, Ronen, Avner, Dagot, Christophe, Hill, Colin, Vaizel-Ohayon, Dalit, Morgenroth, Eberhard, Bertuzzo, Enrico, Wells, George, Kiperwas, Hadas Raanan, Horn, Harald, Negev, Ido, Zucker, Ines, Bar-Or, Itay, Moran-Gilad, Jacob, Balcazar, Jose Luis, Bibby, Kyle, Elimelech, Menachem, Weisbrod, Noam, Nir, Oded, Sued, Oded, Gillor, Osnat, Alvarez, Pedro J., Crameri, Sandra, Arnon, Shai, Walker, Sharon, Yaron, Sima, Nguyen, Thanh H., Berchenko, Yakir, Hu, Yunxia, Ronen, Zeev, and Bar-Zeev, Edo

Published
2020
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29. An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities

Author

O’Sullivan, Denise M., Doyle, Ronan M., Temisak, Sasithon, Redshaw, Nicholas, Whale, Alexandra S., Logan, Grace, Huang, Jiabin, Fischer, Nicole, Amos, Gregory C. A., Preston, Mark D., Marchesi, Julian R., Wagner, Josef, Parkhill, Julian, Motro, Yair, Denise, Hubert, Finn, Robert D., Harris, Kathryn A., Kay, Gemma L., O’Grady, Justin, Ransom-Jones, Emma, Wu, Huihai, Laing, Emma, Studholme, David J., Benavente, Ernest Diez, Phelan, Jody, Clark, Taane G., Moran-Gilad, Jacob, and Huggett, Jim F.

Published
2021
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30. Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study

Author

Cuénod, Aline, Wüthrich, Daniel, Seth-Smith, Helena M. B., Ott, Chantal, Gehringer, Christian, Foucault, Frédéric, Mouchet, Roxanne, Kassim, Ali, Revathi, Gunturu, Vogt, Deborah R., von Felten, Stefanie, Bassetti, Stefano, Tschudin-Sutter, Sarah, Hettich, Timm, Schlotterbeck, Götz, Homberger, Christina, Casanova, Carlo, Moran-Gilad, Jacob, Sagi, Orli, Rodríguez-Sánchez, Belén, Müller, Franco, Aerni, Martina, Gaia, Valeria, van Dessel, Helke, Kampinga, Greetje A., Müller, Claudia, Daubenberger, Claudia, Pflüger, Valentin, and Egli, Adrian

Published
2021
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36. 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 P., Mitsakakis, Konstantinos, Luz, Saturnino, van Belkum, Alex, Becker, Karsten, van den Bruel, Ann, Harbarth, Stephan, Rex, John H., Simonsen, Gunnar Skov, Werner, Guido, Di Gregori, Valentina, Lüdke, Gerd, van Staa, Tjeerd, Moran-Gilad, Jacob, Bachmann, Till T., and on behalf of the JPIAMR AMR-RDT consortium

Published
2019
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39. Premise plumbing bacterial communities in four European cities and their association with Legionella

Author

Scaturro, Maria, primary, Del Chierico, Federica, additional, Motro, Yair, additional, Chaldoupi, Angeliki, additional, Flountzi, Anastasia, additional, Moran-Gilad, Jacob, additional, Girolamo, Antonietta, additional, Koutsiomani, Thomai, additional, Krogulska, Bozena, additional, Lindsay, Diane, additional, Matuszewska, Renata, additional, Papageorgiou, Georgios, additional, Pancer, Katarzyna, additional, Panoussis, Nikolaos, additional, Rota, Maria Cristina, additional, Uldum, Søren Anker, additional, Velonakis, Emmanuel, additional, Chaput, Dominique L., additional, and Ricci, Maria Luisa, additional

Published
2023
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40. A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia

Author

Cuypers, Wim L., primary, Meysman, Pieter, additional, Weill, François-Xavier, additional, Hendriksen, Rene S., additional, Beyene, Getenet, additional, Wain, John, additional, Nair, Satheesh, additional, Chattaway, Marie A., additional, Perez-Sepulveda, Blanca M., additional, Ceyssens, Pieter-Jan, additional, de Block, Tessa, additional, Lee, Winnie W. Y., additional, Pardos de la Gandara, Maria, additional, Kornschober, Christian, additional, Moran-Gilad, Jacob, additional, Veldman, Kees T., additional, Cormican, Martin, additional, Torpdahl, Mia, additional, Fields, Patricia I., additional, Černý, Tomáš, additional, Hardy, Liselotte, additional, Tack, Bieke, additional, Mellor, Kate C., additional, Thomson, Nicholas, additional, Dougan, Gordon, additional, Deborggraeve, Stijn, additional, Jacobs, Jan, additional, Laukens, Kris, additional, and Van Puyvelde, Sandra, additional

Published
2023
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41. Helicobacter cinaediBacteremia in Children: A Case Report and Literature Review

Author

Oren, Itamar, Temper, Violeta, Michael-Gayego, Ayelet, Motro, Yair, Volovelsky, Oded, Moran-Gilad, Jacob, and Gordon, Oren

Abstract

Helicobacter cinaediis known to cause invasive infections in immunocompromised adults. Here we report the first case of H. cinaedibacteremia in a child with nephrotic syndrome. The patient presented with a mild transient febrile illness that resolved spontaneously. We discuss the diagnostic challenges associated with this case and the microbiologic approach, including genomic analysis. Furthermore, we review the current case together with all previous pediatric cases (n = 6). Notably, all cases involved neonates or otherwise immunocompromised individuals and were characterized by severe disease with complicated infections (eg, meningitis, cholangitis and arthritis). H. cinaedibacteremia in children is associated with a wide spectrum of clinical presentations ranging from mild to life-threatening conditions. This bacterium may be difficult to diagnose and require specialized methods.

Published
2024
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43. Bacterial genome wide association study substantiates papGII of Escherichia coli as a patient independent driver of urosepsis

Author

Cuenod, Aline, primary, Agnetti, Jessica, additional, Seth-Smith, Helena, additional, Waelchli, Denise, additional, Scherbakov, Dimitri, additional, Akbergenov, Rashid, additional, Tschudin-Sutter, Sarah, additional, Bassetti, Stefano, additional, Siegemund, Martin, additional, Nickel, Christian H., additional, Moran-Gilad, Jacob, additional, Keys, Timothy G., additional, Pflueger, Valentin, additional, Thomson, Nicholas R, additional, and Egli, Adrian, additional

Published
2023
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44. Wastewater monitoring of SARS-CoV-2 in on-grid, partially and fully off-grid Bedouin communities in Southern Israel

Author

Yaniv, Karin, primary, Craddock, Hillary A., additional, Mahameed, Fareed, additional, Shagan, Marilou, additional, Salah, Ikram, additional, Lakkakula, Satish, additional, Resnick, Keren, additional, Haber, Corinne, additional, Davidovitch, Nadav, additional, Moran-Gilad, Jacob, additional, Kushmaro, Ariel, additional, and Lipchin, Clive, additional

Published
2023
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45. Trends in the Epidemiology of Non-Typhoidal Salmonellosis in Israel between 2010 and 2021

Author

Bassal, Ravit, primary, Davidovich-Cohen, Maya, additional, Yakunin, Eugenia, additional, Rokney, Assaf, additional, Ken-Dror, Shifra, additional, Strauss, Merav, additional, Wolf, Tamar, additional, Sagi, Orli, additional, Amit, Sharon, additional, Moran-Gilad, Jacob, additional, Treygerman, Orit, additional, Karyo, Racheli, additional, Keinan-Boker, Lital, additional, and Cohen, Dani, additional

Published
2023
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46. Lessons Learned from Israel’s Vaccine Rollout

Author

Choi, Yoojin, primary, Stall, Nathan M., additional, Maltsev, Antonina, additional, Bell, Chaim M., additional, Bogoch, Isaac I., additional, Brosh, Tal, additional, Evans, Gerald A., additional, Grill, Allan, additional, Hopkins, Jessica, additional, Kaplan, David M., additional, McGeer, Allison, additional, Moran-Gilad, Jacob, additional, Nowak, Dominik, additional, Presseau, Justin, additional, Salmon, Asher, additional, Schwartz, Brian, additional, and Juni, Peter, additional

Published
2021
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47. Expert guidance on target product profile development for AMR diagnostic tests

Author

Bachmann, Till T., Mitsakakis, Konstantinos, Hays, John P., van Belkum, Alex, Russom, Aman, Luedke, Gerd, Simonsen, Gunnar Skov, Abel, Gyorgy, Peter, Harald, Goossens, Herman, Moran-Gilad, Jacob, Vila, Jordi, Becker, Karsten, Moons, Pieter, Sampath, Rangarajan, Peeling, Rosanna W., Luz, Saturnino, van Staa, Tjeerd, Di Gregori, Valentina, Bachmann, Till T., Mitsakakis, Konstantinos, Hays, John P., van Belkum, Alex, Russom, Aman, Luedke, Gerd, Simonsen, Gunnar Skov, Abel, Gyorgy, Peter, Harald, Goossens, Herman, Moran-Gilad, Jacob, Vila, Jordi, Becker, Karsten, Moons, Pieter, Sampath, Rangarajan, Peeling, Rosanna W., Luz, Saturnino, van Staa, Tjeerd, and Di Gregori, Valentina

Abstract

Diagnostics are widely considered crucial in the fight against antimicrobial resistance (AMR), which is expected to kill 10 million people annually by 2030. Nevertheless, there remains a substantial gap between the need for AMR diagnostics versus their development and implementation. To help address this problem, target product profiles (TPP) have been developed to focus developers’ attention on the key aspects of AMR diagnostic tests. However, during discussion between a multisectoral working group of 51 international experts from industry, academia and healthcare, it was noted that specific AMR-related TPPs could be extended by incorporating the interdependencies between the key characteristics associated with the development of such TPPs. Subsequently, the working group identified 46 characteristics associated with six main categories (ie, Intended Use, Diagnostic Question, Test Description, Assay Protocol, Performance and Commercial). The interdependencies of these characteristics were then identified and mapped against each other to generate new insights for use by stakeholders. Specifically, it may not be possible for diagnostics developers to achieve all of the recommendations in every category of a TPP and this publication indicates how prioritising specific TPP characteristics during diagnostics development may influence (or not) a range of other TPP characteristics associated with the diagnostic. The use of such guidance, in conjunction with specific TPPs, could lead to more efficient AMR diagnostics development., QC 20240118

Published
2023
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48. A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia

Author

Cuypers, Wim L., Meysman, Pieter, Weill, François-Xavier, Hendriksen, Rene S., Beyene, Getenet, Wain, John, Nair, Satheesh, Chattaway, Marie A., Perez-Sepulveda, Blanca M., Ceyssens, Pieter-Jan, de Block, Tessa, Lee, Winnie W. Y., Pardos de la Gandara, Maria, Kornschober, Christian, Moran-Gilad, Jacob, Veldman, Kees T., Cormican, Martin, Torpdahl, Mia, Fields, Patricia I., Černý, Tomáš, Hardy, Liselotte, Tack, Bieke, Mellor, Kate C., Thomson, Nicholas, Dougan, Gordon, Deborggraeve, Stijn, Jacobs, Jan, Laukens, Kris, Van Puyvelde, Sandra, Cuypers, Wim L., Meysman, Pieter, Weill, François-Xavier, Hendriksen, Rene S., Beyene, Getenet, Wain, John, Nair, Satheesh, Chattaway, Marie A., Perez-Sepulveda, Blanca M., Ceyssens, Pieter-Jan, de Block, Tessa, Lee, Winnie W. Y., Pardos de la Gandara, Maria, Kornschober, Christian, Moran-Gilad, Jacob, Veldman, Kees T., Cormican, Martin, Torpdahl, Mia, Fields, Patricia I., Černý, Tomáš, Hardy, Liselotte, Tack, Bieke, Mellor, Kate C., Thomson, Nicholas, Dougan, Gordon, Deborggraeve, Stijn, Jacobs, Jan, Laukens, Kris, and Van Puyvelde, Sandra

Abstract

Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance.

Published
2023

49. Quality of MALDI-TOF mass spectra in routine diagnostics:results from an international external quality assessment including 36 laboratories from 12 countries using 47 challenging bacterial strains

Author

Cuénod, Aline, Aerni, Martina, Bagutti, Claudia, Bayraktar, Banu, Boz, Efe Serkan, Carneiro, Cynthia Beisert, Casanova, Carlo, Coste, Alix T., Damborg, Peter, van Dam, Dirk W., Demirci, Mehmet, Drevinek, Pavel, Dubuis, Olivier, Fernandez, José, Greub, Gilbert, Hrabak, Jaroslav, Hürkal Yiğitler, Gülen, Hurych, Jakub, Jensen, Thøger Gorm, Jost, Géraldine, Kampinga, Greetje A., Kittl, Sonja, Lammens, Christine, Lang, Claudia, Lienhard, Reto, Logan, Julie, Maffioli, Carola, Mareković, Ivana, Marschal, Matthias, Moran-Gilad, Jacob, Nolte, Oliver, Oberle, Michael, Pedersen, Michael, Pflüger, Valentin, Pranghofer, Sigrid, Reichl, Julia, Rentenaar, Rob J., Riat, Arnaud, Rodríguez-Sánchez, Belén, Schilt, Camille, Schlotterbeck, Ann Kathrin, Schrenzel, Jacques, Troib, Shani, Willems, Elise, Wootton, Mandy, Ziegler, Dominik, Egli, Adrian, Cuénod, Aline, Aerni, Martina, Bagutti, Claudia, Bayraktar, Banu, Boz, Efe Serkan, Carneiro, Cynthia Beisert, Casanova, Carlo, Coste, Alix T., Damborg, Peter, van Dam, Dirk W., Demirci, Mehmet, Drevinek, Pavel, Dubuis, Olivier, Fernandez, José, Greub, Gilbert, Hrabak, Jaroslav, Hürkal Yiğitler, Gülen, Hurych, Jakub, Jensen, Thøger Gorm, Jost, Géraldine, Kampinga, Greetje A., Kittl, Sonja, Lammens, Christine, Lang, Claudia, Lienhard, Reto, Logan, Julie, Maffioli, Carola, Mareković, Ivana, Marschal, Matthias, Moran-Gilad, Jacob, Nolte, Oliver, Oberle, Michael, Pedersen, Michael, Pflüger, Valentin, Pranghofer, Sigrid, Reichl, Julia, Rentenaar, Rob J., Riat, Arnaud, Rodríguez-Sánchez, Belén, Schilt, Camille, Schlotterbeck, Ann Kathrin, Schrenzel, Jacques, Troib, Shani, Willems, Elise, Wootton, Mandy, Ziegler, Dominik, and Egli, Adrian

Abstract

Objectives: Matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a widely used method for bacterial species identification. Incomplete databases and mass spectral quality (MSQ) still represent major challenges. Important proxies for MSQ are the number of detected marker masses, reproducibility, and measurement precision. We aimed to assess MSQs across diagnostic laboratories and the potential of simple workflow adaptations to improve it. Methods: For baseline MSQ assessment, 47 diverse bacterial strains, which are challenging to identify by MALDI-TOF MS, were routinely measured in 36 laboratories from 12 countries, and well-defined MSQ features were used. After an intervention consisting of detailed reported feedback and instructions on how to acquire MALDI-TOF mass spectra, measurements were repeated and MSQs were compared. Results: At baseline, we observed heterogeneous MSQ between the devices, considering the median number of marker masses detected (range = [2–25]), reproducibility between technical replicates (range = [55%–86%]), and measurement error (range = [147 parts per million (ppm)–588 ppm]). As a general trend, the spectral quality was improved after the intervention for devices, which yielded low MSQs in the baseline assessment as follows: for four out of five devices with a high measurement error, the measurement precision was improved (p-values <0.001, paired Wilcoxon test); for six out of ten devices, which detected a low number of marker masses, the number of detected marker masses increased (p-values <0.001, paired Wilcoxon test). Discussion: We have identified simple workflow adaptations, which, to some extent, improve MSQ of poorly performing devices and should be considered by laboratories yielding a low MSQ. Improving MALDI-TOF MSQ in routine diagnostics is essential for increasing the resolution of bacterial identification by MALDI-TOF MS, which is dependent on the reproducible detection of

Published
2023

50. Bacterial genome-wide association study substantiates papGII of Escherichia coli as a major risk factor for urosepsis

Author

Cuénod, Aline; https://orcid.org/0000-0002-8522-6134, Agnetti, Jessica, Seth-Smith, Helena M B, Roloff, Tim, Wälchli, Denise, Shcherbakov, Dimitri, Akbergenov, Rashid, Tschudin-Sutter, Sarah, Bassetti, Stefano, Siegemund, Martin, Nickel, Christian H, Moran-Gilad, Jacob, Keys, Timothy G, Pflüger, Valentin, Thomson, Nicholas R, Egli, Adrian, Cuénod, Aline; https://orcid.org/0000-0002-8522-6134, Agnetti, Jessica, Seth-Smith, Helena M B, Roloff, Tim, Wälchli, Denise, Shcherbakov, Dimitri, Akbergenov, Rashid, Tschudin-Sutter, Sarah, Bassetti, Stefano, Siegemund, Martin, Nickel, Christian H, Moran-Gilad, Jacob, Keys, Timothy G, Pflüger, Valentin, Thomson, Nicholas R, and Egli, Adrian

Abstract

BACKGROUND Urinary tract infections (UTIs) are among the most common bacterial infections worldwide, often caused by uropathogenic Escherichia coli. Multiple bacterial virulence factors or patient characteristics have been linked separately to progressive, more invasive infections. In this study, we aim to identify pathogen- and patient-specific factors that drive the progression to urosepsis by jointly analysing bacterial and host characteristics. METHODS We analysed 1076 E. coli strains isolated from 825 clinical cases with UTI and/or bacteraemia by whole-genome sequencing (Illumina). Sequence types (STs) were determined via srst2 and capsule loci via fastKaptive. We compared the isolates from urine and blood to confirm clonality. Furthermore, we performed a bacterial genome-wide association study (bGWAS) (pyseer) using bacteraemia as the primary clinical outcome. Clinical data were collected by an electronic patient chart review. We concurrently analysed the association of the most significant bGWAS hit and important patient characteristics with the clinical endpoint bacteraemia using a generalised linear model (GLM). Finally, we designed qPCR primers and probes to detect papGII-positive E. coli strains and prospectively screened E. coli from urine samples (n = 1657) at two healthcare centres. RESULTS Our patient cohort had a median age of 75.3 years (range: 18.00-103.1) and was predominantly female (574/825, 69.6%). The bacterial phylogroups B2 (60.6%; 500/825) and D (16.6%; 137/825), which are associated with extraintestinal infections, represent the majority of the strains in our collection, many of which encode a polysaccharide capsule (63.4%; 525/825). The most frequently observed STs were ST131 (12.7%; 105/825), ST69 (11.0%; 91/825), and ST73 (10.2%; 84/825). Of interest, in 12.3% (13/106) of cases, the E. coli pairs in urine and blood were only distantly related. In line with previous bGWAS studies, we identified the gene papGII (p-value < 0.001), which en

Published
2023

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