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2. Evaluating Large Language Models for Public Health Classification and Extraction Tasks

Author

Harris, Joshua, Laurence, Timothy, Loman, Leo, Grayson, Fan, Nonnenmacher, Toby, Long, Harry, WalsGriffith, Loes, Douglas, Amy, Fountain, Holly, Georgiou, Stelios, Hardstaff, Jo, Hopkins, Kathryn, Chi, Y-Ling, Kuyumdzhieva, Galena, Larkin, Lesley, Collins, Samuel, Mohammed, Hamish, Finnie, Thomas, Hounsome, Luke, and Riley, Steven

Subjects
Computer Science - Computation and Language, Computer Science - Machine Learning, 68T50
Abstract

Advances in Large Language Models (LLMs) have led to significant interest in their potential to support human experts across a range of domains, including public health. In this work we present automated evaluations of LLMs for public health tasks involving the classification and extraction of free text. We combine six externally annotated datasets with seven new internally annotated datasets to evaluate LLMs for processing text related to: health burden, epidemiological risk factors, and public health interventions. We initially evaluate five open-weight LLMs (7-70 billion parameters) across all tasks using zero-shot in-context learning. We find that Llama-3-70B-Instruct is the highest performing model, achieving the best results on 15/17 tasks (using micro-F1 scores). We see significant variation across tasks with all open-weight LLMs scoring below 60% micro-F1 on some challenging tasks, such as Contact Classification, while all LLMs achieve greater than 80% micro-F1 on others, such as GI Illness Classification. For a subset of 12 tasks, we also evaluate GPT-4 and find comparable results to Llama-3-70B-Instruct, which scores equally or outperforms GPT-4 on 6 of the 12 tasks. Overall, based on these initial results we find promising signs that LLMs may be useful tools for public health experts to extract information from a wide variety of free text sources, and support public health surveillance, research, and interventions., Comment: 33 pages. Feedback and comments are highly appreciated

Published
2024

8. Presence of phage-plasmids in multiple serovars of Salmonella enterica

Author

Nair, Satheesh, primary, Barker, Clare R., additional, Bird, Matthew, additional, Greig, David R., additional, Collins, Caitlin, additional, Painset, Anaïs, additional, Chattaway, Marie, additional, Pickard, Derek, additional, Larkin, Lesley, additional, Gharbia, Saheer, additional, Didelot, Xavier, additional, and Ribeca, Paolo, additional

Published
2024
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9. A genetically related cluster of Salmonella Typhimurium cases in humans associated with ruminant livestock and related food chains, United Kingdom, August 2021-December 2022

Author

Merrick, Rachel, primary, Pulford, Caisey, additional, Rubeshkumar, Polani, additional, Seyan, Parnam, additional, Fina, Laia, additional, Sawyer, Clare, additional, Pacchiarini, Nicole, additional, Pollock, Carrie, additional, Lighthill, Jonathan, additional, Potter, Tina, additional, Harvey, Nathan, additional, Thomas, Kara, additional, Lloyd, Daniel, additional, Gherman, Iulia, additional, Mackintosh, Adrienne, additional, Lawes, Joanna, additional, Snow, Lucy, additional, Waldram, Alison, additional, Larkin, Lesley, additional, Balasegaram, Sooria, additional, Painset, Anais, additional, McCormick, Jacquelyn, additional, Elson, Richard, additional, Browning, Lynda, additional, Williams, Christopher, additional, Andrew, Rachel, additional, Mably, Susan, additional, and Thomas, Daniel, additional

Published
2024
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13. An international outbreak of Salmonella enterica serotype Enteritidis linked to eggs from Poland: a microbiological and epidemiological study

Author

Bertrand, Sophie, Brennan, Martine, Browning, Lynda, Bruce, Ryan, Cantaert, Vera, Chattaway, Marie, Coia, John, Couper, Sarah, Žohar Čretnik, Tjaša, Daniel, Ondřej, Dionisi, Anna Maria, Fabre, Laetitia, Fitz-James, Ife, Florek, Karolina, Florianová, Martina, Fox, Eithne, Frelih, Tatjana, Grilc, Eva, Katalinic Jankovic, Vera, Jourdan, Nathalie, Karpíšková, Renata, van den Kerkhof, Hans, Kuiling, Sjoerd, Kurečić Filipović, Sanja, Laisnez, Valeska, Lange, Heidi, deLappes, Niall, Leblanc, Judith, Luzzi, Ida, Mandilara, Georgia, Mather, Henry, Mattheus, Wesley, Mellou, Kassiani, Morgan, Deborah, Pászti, Judit, de Pinna, Elizabeth, Ragimbeau, Catherine, Røed, Margrethe Hovda, Salmenlinna, Saara, Smith, Robert, Smith-Palmer, Alison, Špačková, Michaela, Torpdahl, Mia, Trkov, Marija, Trönnberg, Linda, Tzani, Myrsini, Utsi, Lara, Wasyl, Dariusz, Weicherding, Pierre, Pijnacker, Roan, Dallman, Timothy J, Tijsma, Aloys S L, Hawkins, Gillian, Larkin, Lesley, Kotila, Saara M, Amore, Giusi, Amato, Ettore, Suzuki, Pamina M, Denayer, Sarah, Klamer, Sofieke, McCormick, Jacquelyn, Hartman, Hassan, Hughes, Gareth J, Brandal, Lin C T, Brown, Derek, Mossong, Joël, Jernberg, Cecilia, Müller, Luise, Palm, Daniel, Severi, Ettore, Gołębiowska, Joannna, Hunjak, Blaženka, Owczarek, Slawomir, Le Hello, Simon, Garvey, Patricia, Mooijman, Kirsten, Friesema, Ingrid H M, van der Weijden, Coen, van der Voort, Menno, Rizzi, Valentina, and Franz, Eelco

Published
2019
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17. Foodborne Outbreak of Extended Spectrum Beta-lactamase Producing Shigella sonnei Associated with Contaminated Spring Onions in the United Kingdom

Author

Jenkins, Claire, primary, Griffith, Philippa, additional, Hoban, Ann, additional, Brown, Claire, additional, Garner, Joanna, additional, Bardsley, Megan, additional, Willis, Caroline, additional, Jorgensen, Frieda, additional, Bird, Matthew, additional, Greig, David R., additional, Edmunds, Matt, additional, Beck, Charles, additional, and Larkin, Lesley, additional

Published
2023
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19. Investigation of an international outbreak of multidrug-resistant monophasic Typhimurium associated with chocolate products, EU/EEA and United Kingdom, February to April 2022

Author

Larkin, Lesley, Pardos de la Gandara, Maria, Hoban, Ann, Pulford, Caisey, Jourdan-Da Silva, Nathalie, de Valk, Henriette, Browning, Lynda, Falkenhorst, Gerhard, Simon, Sandra, Lachmann, Raskit, Dryselius, Rikard, Karamehmedovic, Nadja, Börjesson, Stefan, van Cauteren, Dieter, Laisnez, Valeska, Mattheus, Wesley, Pijnacker, Roan, van den Beld, Maaike, Mossong, Joël, Ragimbeau, Catherine, Vergison, Anne, Thorstensen Brandal, Lin, Lange, Heidi, Garvey, Patricia, Nielsen, Charlotte Salgaard, Herrera León, Silvia, Varela, Carmen, Chattaway, Marie, Weill, François-Xavier, Brown, Derek, and McKeown, Paul

Subjects
Monophasic Salmonella Typhimurium, whole genome sequencing, antimicrobial resistance profile, outbreak, chocolate products, multi-country collaboration, descriptive epidemiological evidence, core-genome multi locus sequence typing
Abstract

An extensive multi-country outbreak of multidrug-resistant monophasic Salmonella Typhimurium infection in 10 countries with 150 reported cases, predominantly affecting young children, has been linked to chocolate products produced by a large multinational company. Extensive withdrawals and recalls of multiple product lines have been undertaken. With Easter approaching, widespread product distribution and the vulnerability of the affected population, early and effective real-time sharing of microbiological and epidemiological information has been of critical importance in effectively managing this serious food-borne incident.

Published
2022

20. Levels and genotypes of Salmonella and levels of Escherichia coli in frozen ready-to-cook chicken and turkey products in England tested in 2020 in relation to an outbreak of S. Enteritidis

Author

Jørgensen, Frieda, primary, McLauchlin, Jim, additional, Verlander, Neville Q., additional, Aird, Heather, additional, Balasegaram, Sooria, additional, Chattaway, Marie Anne, additional, Dallman, Tim, additional, Herdman, M. Trent, additional, Hoban, Ann, additional, Lai, Sandra, additional, Larkin, Lesley, additional, McCormick, Jacquelyn, additional, Reeves, Lorraine Sadler, additional, and Willis, Caroline, additional

Published
2022
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21. Investigation of an international outbreak of multidrug-resistant monophasic Salmonella Typhimurium associated with chocolate products, EU/EEA and United Kingdom, February to April 2022

Author

Larkin, Lesley, primary, Pardos de la Gandara, Maria, additional, Hoban, Ann, additional, Pulford, Caisey, additional, Jourdan-Da Silva, Nathalie, additional, de Valk, Henriette, additional, Browning, Lynda, additional, Falkenhorst, Gerhard, additional, Simon, Sandra, additional, Lachmann, Raskit, additional, Dryselius, Rikard, additional, Karamehmedovic, Nadja, additional, Börjesson, Stefan, additional, van Cauteren, Dieter, additional, Laisnez, Valeska, additional, Mattheus, Wesley, additional, Pijnacker, Roan, additional, van den Beld, Maaike, additional, Mossong, Joël, additional, Ragimbeau, Catherine, additional, Vergison, Anne, additional, Thorstensen Brandal, Lin, additional, Lange, Heidi, additional, Garvey, Patricia, additional, Nielsen, Charlotte Salgaard, additional, Herrera León, Silvia, additional, Varela, Carmen, additional, Chattaway, Marie, additional, Weill, François-Xavier, additional, Brown, Derek, additional, and McKeown, Paul, additional

Published
2022
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25. Salmonella enterica serovar Enteritidis, England and Wales, 1945-2011

Author

Lane, Christopher R., LeBaigue, Susan, Esan, Oluwaseun B., Awofisyo, Adedoyin A., Adams, Natalie L., Fisher, Ian S.T., Grant, Kathie A., Peters, Tansy M., Larkin, Lesley, Davies, Robert H., and Adak, Goutam K.

Subjects
Poultry industry -- Health aspects, Infection -- Health aspects, Salmonella -- Health aspects, Health
Abstract

A pandemic of Salmonella enterica serovar Enteritidis infection was recognized by epidemiologists in the United States in the late 1970s; a 6-fold rise in these infections was observed in northeastern [...]

Published
2014
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27. Deliverable JIP1-2.7 Revised OH Knowledge Base - Epi, including lessons learned from the OH pilots

Author

Gethmann, Jörn, Selhorst, Thomas, Dups-Bergmann, Johanna, Ellis-Iversen, Johanne, Friesema, Ingrid, Lagesen, Karin, Dórea, Fernanda, Kuhn, Katrin, Dispas, Marc, Gonzales Rojas, Jose, Jore, Solveig, Jernberg, Cecilia, Cook, Charlotte, and Larkin, Lesley

Subjects
Knowledge base, ORION, Surveillance inventory, Statistical analysis, One Health
Abstract

OHEJP Project ORION - Workpackage 2 - Epi REVISED OH KNOWLEDGE BASE - EPI, INCLUDING LESSONS LEARNED FROM THE OH PILOTS: - TOXOPLASMA GONDII PILOT STUDIES - Towards a One Health surveillance of hepatitis E in the Netherlands - Promoting the implementation of One Health collaborative approaches between disciplines in Belgium with a focus on the elaboration of the future national One Health Antimicrobial report using qualitative research methodologies - WP2EPI: RASCH MODEL

Published
2021
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28. Deliverable JIP1-2.8 - Status report on OH Knowledge Base - NGS

Author

Lagesen, Karin, Naseer, Umaer, Macdonald, Emily, Brandal, Lin, Skjerdal, Olaug Taran, Haverkamp, Thomas H.A., Fiskebeck, Eve Zeyl, Samy, Jeevan Karloss Antony, Marselis, Georgios, Sekse, Camilla, Kaspersen, Håkon, Cha, Wonhee, Jernberg, Cecilia, Svartstrom, Olov, Torpdahl, Mia, Nielsen, Eva Møller, Larkin, Lesley, Cook, Charlotte, Withenshaw, Susan, and Lawes, Johanna

Subjects
ORION, NGS
Abstract

OHEJP Project ORION

Published
2021
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29. Deliverable JIP1-3.3 Revised OH Harmonisation Infrastructure Hub, including lessons learned from the OH pilots

Author

Dórea, Fernanda, Günther, Taras, López de Abechuco, Estíbaliz, Holmberg, Mia, Jernberg, Cecilia, Hjertkvist, Marika, Filter, Matthias, Foddai, Alessandro, Ellis-Iversen, Johanne, Cook, Charlotte, Lawes, Johanna, Larkin, Lesley, Friesema, Ingrid, Filippitz, Maria-Eleni, Cargnel, Mickael, Boseret, Geraldine, and Lagesen, Karin

Subjects
ORION, Ontology, Linked Data, Interoperability
Abstract

OHEJP Project ORION - Workpackage 3 TOWARDS AN INTEROPERABLE ONE HEALTH DATA INFRASTRUCTURE

Published
2021
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31. Predicted Norovirus Resurgence in 2021-2022 Due to the Relaxation of Nonpharmaceutical Interventions Associated with COVID-19 Restrictions in England: A Mathematical Modelling Study

Author

O’Reilly, Kathleen M, primary, Sandman, Frank, additional, Allen, David, additional, Jarvis, Christopher I, additional, Gimma, Amy, additional, Douglas, Amy, additional, Larkin, Lesley, additional, Wong, Kerry LM, additional, Baguelin, Marc, additional, Baric, Ralph S, additional, Lindesmith, Lisa C, additional, Goldstein, Richard A, additional, Breuer, Judith, additional, and Edmunds, W John, additional

Published
2021
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32. Additional file 4 of Predicted norovirus resurgence in 2021���2022 due to the relaxation of nonpharmaceutical interventions associated with COVID-19 restrictions in England: a mathematical modeling study

Author

O���Reilly, Kathleen M., Sandman, Frank, Allen, David, Jarvis, Christopher I., Gimma, Amy, Douglas, Amy, Larkin, Lesley, Wong, Kerry L. M., Baguelin, Marc, Baric, Ralph S., Lindesmith, Lisa C., Goldstein, Richard A., Breuer, Judith, and Edmunds, W. John

Abstract

Additional file 4.. Details of ���Polymod��� and ���Comix��� contact matrices.

Published
2021
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33. Additional file 3 of Predicted norovirus resurgence in 2021���2022 due to the relaxation of nonpharmaceutical interventions associated with COVID-19 restrictions in England: a mathematical modeling study

Author

O���Reilly, Kathleen M., Sandman, Frank, Allen, David, Jarvis, Christopher I., Gimma, Amy, Douglas, Amy, Larkin, Lesley, Wong, Kerry L. M., Baguelin, Marc, Baric, Ralph S., Lindesmith, Lisa C., Goldstein, Richard A., Breuer, Judith, and Edmunds, W. John

Abstract

Additional file 3.. Alternative model assumptions for norovirus.

Published
2021
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34. Additional file 2 of Predicted norovirus resurgence in 2021���2022 due to the relaxation of nonpharmaceutical interventions associated with COVID-19 restrictions in England: a mathematical modeling study

Author

O���Reilly, Kathleen M., Sandman, Frank, Allen, David, Jarvis, Christopher I., Gimma, Amy, Douglas, Amy, Larkin, Lesley, Wong, Kerry L. M., Baguelin, Marc, Baric, Ralph S., Lindesmith, Lisa C., Goldstein, Richard A., Breuer, Judith, and Edmunds, W. John

Subjects
Data_FILES
Abstract

Additional file 2. Description of the model fitting procedure.

Published
2021
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35. Additional file 1 of Predicted norovirus resurgence in 2021���2022 due to the relaxation of nonpharmaceutical interventions associated with COVID-19 restrictions in England: a mathematical modeling study

Author

O���Reilly, Kathleen M., Sandman, Frank, Allen, David, Jarvis, Christopher I., Gimma, Amy, Douglas, Amy, Larkin, Lesley, Wong, Kerry L. M., Baguelin, Marc, Baric, Ralph S., Lindesmith, Lisa C., Goldstein, Richard A., Breuer, Judith, and Edmunds, W. John

Abstract

Additional file 1: Full description of the mathematical model for norovirus. Table S1. Parameters within the mathematical model for norovirus and sources of values used.

Published
2021
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36. "Then Her World Exploded": Science-Fictional Reading and Ta-Nehisi Coates's Between the World and Me.

Author

Larkin, Lesley

Subjects
SCIENCE fiction, AFRICAN American literature, ANTI-Black racism
Abstract

This essay advances science-fictional reading as a crucial practice for Black literary studies, one that can be applied to a wide variety of texts, including essay and memoir. Science-fictional reading, as outlined here, is more than just the critical counterpart to science-fictional form. Although honed by reading science fiction, it is an interpretive approach that does not depend on the genre classification of its object; rather, it presumes that speculative aspects inhere in all literary works, not least those tied to racial justice movements. Three science fictional reading practices are explored in detail: recognizing science-fictional tropes and techniques in non-science fictional texts, being open to semantic play, and tracking the distance between the world of the text and the world of the reader. These practices pay off substantially when brought to bear on Ta-Nehisi Coates's 2015 Between the World and Me , a nonfiction work that articulates an approach to literary study aligned with science-fictional reading, despite not being a work of science fiction itself. As the analysis of Coates's work makes clear, science-fictional reading can illuminate the distance between a nonfictional account of antiblack violence (that is, the real world) and the fictions that sustain that violence (that is, the imagined world some readers believe they inhabit). Recognizing the distance between one world and the other is a vital step in the project of racial justice that animates so much Black literature and criticism. [ABSTRACT FROM AUTHOR]

Published
2022
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37. Investigation of an international outbreak of multidrugresistant monophasic Salmonella Typhimurium associated with chocolate products, EU/EEA and United Kingdom, February to April 2022.

Author

Larkin, Lesley, Pardos de la Gandara, Maria, Hoban, Ann, Pulford, Caisey, Silva, Nathalie Jourdan-Da, de Valk, Henriette, Browning, Lynda, Falkenhorst, Gerhard, Simon, Sandra, Lachmann, Raskit, Dryselius, Rikard, Karamehmedovic, Nadja, Börjesson, Stefan, van Cauteren, Dieter, Laisnez, Valeska, Mattheus, Wesley, Pijnacker, Roan, van den Beld, Maaike, Mossong, Joël, and Ragimbeau, Catherine

Published
2022
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39. The Transformation of Reference Microbiology Methods and Surveillance for Salmonella With the Use of Whole Genome Sequencing in England and Wales

Author

Chattaway, Marie Anne, primary, Dallman, Timothy J., additional, Larkin, Lesley, additional, Nair, Satheesh, additional, McCormick, Jacquelyn, additional, Mikhail, Amy, additional, Hartman, Hassan, additional, Godbole, Gauri, additional, Powell, David, additional, Day, Martin, additional, Smith, Robert, additional, and Grant, Kathie, additional

Published
2019
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40. Predicted norovirus resurgence in 2021-2022 due to the relaxation of nonpharmaceutical interventions associated with COVID-19 restrictions in England: a mathematical modeling study.

Author

O'Reilly, Kathleen M., Sandman, Frank, Allen, David, Jarvis, Christopher I., Gimma, Amy, Douglas, Amy, Larkin, Lesley, Wong, Kerry L. M., Baguelin, Marc, Baric, Ralph S., Lindesmith, Lisa C., Goldstein, Richard A., Breuer, Judith, and Edmunds, W. John

Subjects
NOROVIRUS diseases, COVID-19, NON-communicable diseases, ENDEMIC diseases, MATHEMATICAL models, COMMUNICABLE diseases
Abstract

Background: To reduce the coronavirus disease burden in England, along with many other countries, the government implemented a package of non-pharmaceutical interventions (NPIs) that have also impacted other transmissible infectious diseases such as norovirus. It is unclear what future norovirus disease incidence is likely to look like upon lifting these restrictions.Methods: Here we use a mathematical model of norovirus fitted to community incidence data in England to project forward expected incidence based on contact surveys that have been collected throughout 2020-2021.Results: We report that susceptibility to norovirus infection has likely increased between March 2020 and mid-2021. Depending upon assumptions of future contact patterns incidence of norovirus that is similar to pre-pandemic levels or an increase beyond what has been previously reported is likely to occur once restrictions are lifted. Should adult contact patterns return to 80% of pre-pandemic levels, the incidence of norovirus will be similar to previous years. If contact patterns return to pre-pandemic levels, there is a potential for the expected annual incidence to be up to 2-fold larger than in a typical year. The age-specific incidence is similar across all ages.Conclusions: Continued national surveillance for endemic diseases such as norovirus will be essential after NPIs are lifted to allow healthcare services to adequately prepare for a potential increase in cases and hospital pressures beyond what is typically experienced. [ABSTRACT FROM AUTHOR]

Published
2021
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41. An international outbreak of Salmonella enterica serotype Enteritidis linked to eggs from Poland: a microbiological and epidemiological study

Author

Pijnacker, Roan, Dallman, Timothy J, Tijsma, Aloys S L, Hawkins, Gillian, Larkin, Lesley, Kotila, Saara M, Amore, Giusi, Amato, Ettore, Suzuki, Pamina M, Denayer, Sarah, Klamer, Sofieke, Pászti, Judit, McCormick, Jacquelyn, Hartman, Hassan, Hughes, Gareth J, Brandal, Lin C T, Brown, Derek, Mossong, Joël, Jernberg, Cecilia, Müller, Luise, Palm, Daniel, Severi, Ettore, Gołębiowska, Joannna, Hunjak, Blaženka, Owczarek, Slawomir, Le Hello, Simon, Garvey, Patricia, Mooijman, Kirsten, Friesema, Ingrid H M, van der Weijden, Coen, van der Voort, Menno, Rizzi, Valentina, and Franz, Eelco

Published
2019

42. Salmonellosis outbreak with novel Salmonella enterica subspecies enterica serotype (11:z41:e,n,z15) attributable to sesame products in five European countries, 2016 to 2017

Author

Meinen, Anika Simon, Sandra Banerji, Sangeeta Szabo, Istvan and Malorny, Burkhard Borowiak, Maria Hadziabdic, Sead and Becker, Natalie Luber, Petra Lohr, Dorothee Harms, Carolin and Plenge-Boenig, Anita Mellou, Kassiani Mandilara, Georgia and Mossong, Joel Ragimbeau, Catherine Weicherding, Pierre Hau, Patrick Dedicova, Daniela Safarikova, Lucie Nair, Satheesh and Dallman, Timothy J. Larkin, Lesley McCormick, Jacquelyn and De Pinna, Elizabeth Severi, Ettore Kotila, Saara Niskanen, Taina Rizzi, Valentina Deserio, Domenico Flieger, Antje and Stark, Klaus

Abstract

In spring 2016, Greece reported an outbreak caused by a previously undescribed Salmonella enterica subsp. enterica serotype (antigenic formula 11:z41:e,n,z15) via the Epidemic Intelligence Information System for Food-and Waterborne Diseases and Zoonoses (EPIS-FWD), with epidemiological evidence for sesame products as presumptive vehicle. Subsequently, Germany, Czech Republic, Luxembourg and the United Kingdom (UK) reported infections with this novel serotype via EPIS-FWD. Concerned countries in collaboration with the European Centre for Disease Prevention and Control (ECDC) and European Food Safety Authority (EFSA) adopted a common outbreak case definition. An outbreak case was defined as a laboratory-confirmed notification of the novel Salmonella serotype. Between March 2016 and April 2017, 47 outbreak cases were notified (Greece: n = 22; Germany: n = 13; Czech Republic: n = 5; Luxembourg: n = 4; UK: n = 3). Whole genome sequencing revealed the very close genetic relatedness of isolates from all affected countries. Interviews focusing on sesame product consumption, suspicious food item testing and trace-back analysis following Salmonella spp. detection in food products identified a company in Greece where sesame seeds from different countries were processed. Through European collaboration, it was possible to identify and recall sesame spread as one contaminated food item serving as vehicle of infection and trace it back to its origin.

Published
2019

43. Salmonellosis outbreak with novel Salmonella enterica subspecies enterica serotype (11:z41:e,n,z15) attributable to sesame products in five European countries, 2016 to 2017

Author

Meinen, Anika, primary, Simon, Sandra, additional, Banerji, Sangeeta, additional, Szabo, Istvan, additional, Malorny, Burkhard, additional, Borowiak, Maria, additional, Hadziabdic, Sead, additional, Becker, Natalie, additional, Luber, Petra, additional, Lohr, Dorothee, additional, Harms, Carolin, additional, Plenge-Bönig, Anita, additional, Mellou, Kassiani, additional, Mandilara, Georgia, additional, Mossong, Joël, additional, Ragimbeau, Catherine, additional, Weicherding, Pierre, additional, Hau, Patrick, additional, Dědičová, Daniela, additional, Šafaříková, Lucie, additional, Nair, Satheesh, additional, Dallman, Timothy J, additional, Larkin, Lesley, additional, McCormick, Jacquelyn, additional, De Pinna, Elizabeth, additional, Severi, Ettore, additional, Kotila, Saara, additional, Niskanen, Taina, additional, Rizzi, Valentina, additional, Deserio, Domenico, additional, Flieger, Antje, additional, and Stark, Klaus, additional

Published
2019
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44. An international outbreak of Salmonella enterica serotype Enteritidis linked to eggs from Poland: a microbiological and epidemiological study

Author

Pijnacker, Roan, primary, Dallman, Timothy J, additional, Tijsma, Aloys S L, additional, Hawkins, Gillian, additional, Larkin, Lesley, additional, Kotila, Saara M, additional, Amore, Giusi, additional, Amato, Ettore, additional, Suzuki, Pamina M, additional, Denayer, Sarah, additional, Klamer, Sofieke, additional, Pászti, Judit, additional, McCormick, Jacquelyn, additional, Hartman, Hassan, additional, Hughes, Gareth J, additional, Brandal, Lin C T, additional, Brown, Derek, additional, Mossong, Joël, additional, Jernberg, Cecilia, additional, Müller, Luise, additional, Palm, Daniel, additional, Severi, Ettore, additional, Gołębiowska, Joannna, additional, Hunjak, Blaženka, additional, Owczarek, Slawomir, additional, Le Hello, Simon, additional, Garvey, Patricia, additional, Mooijman, Kirsten, additional, Friesema, Ingrid H M, additional, van der Weijden, Coen, additional, van der Voort, Menno, additional, Rizzi, Valentina, additional, Franz, Eelco, additional, Bertrand, Sophie, additional, Brennan, Martine, additional, Browning, Lynda, additional, Bruce, Ryan, additional, Cantaert, Vera, additional, Chattaway, Marie, additional, Coia, John, additional, Couper, Sarah, additional, Žohar Čretnik, Tjaša, additional, Daniel, Ondřej, additional, Dionisi, Anna Maria, additional, Fabre, Laetitia, additional, Fitz-James, Ife, additional, Florek, Karolina, additional, Florianová, Martina, additional, Fox, Eithne, additional, Frelih, Tatjana, additional, Grilc, Eva, additional, Katalinic Jankovic, Vera, additional, Jourdan, Nathalie, additional, Karpíšková, Renata, additional, van den Kerkhof, Hans, additional, Kuiling, Sjoerd, additional, Kurečić Filipović, Sanja, additional, Laisnez, Valeska, additional, Lange, Heidi, additional, deLappes, Niall, additional, Leblanc, Judith, additional, Luzzi, Ida, additional, Mandilara, Georgia, additional, Mather, Henry, additional, Mattheus, Wesley, additional, Mellou, Kassiani, additional, Morgan, Deborah, additional, de Pinna, Elizabeth, additional, Ragimbeau, Catherine, additional, Røed, Margrethe Hovda, additional, Salmenlinna, Saara, additional, Smith, Robert, additional, Smith-Palmer, Alison, additional, Špačková, Michaela, additional, Torpdahl, Mia, additional, Trkov, Marija, additional, Trönnberg, Linda, additional, Tzani, Myrsini, additional, Utsi, Lara, additional, Wasyl, Dariusz, additional, and Weicherding, Pierre, additional

Published
2019
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45. Emergence of phylogenetically diverse and fluoroquinolone resistant Salmonella Enteritidis as a cause of invasive nontyphoidal Salmonella disease in Ghana

Author

Aldrich, Cassandra, primary, Hartman, Hassan, additional, Feasey, Nicholas, additional, Chattaway, Marie Anne, additional, Dekker, Denise, additional, Al-Emran, Hassan M., additional, Larkin, Lesley, additional, McCormick, Jacquelyn, additional, Sarpong, Nimako, additional, Le Hello, Simon, additional, Adu-Sarkodie, Yaw, additional, Panzner, Ursula, additional, Park, Se Eun, additional, Im, Justin, additional, Marks, Florian, additional, May, Jürgen, additional, Dallman, Timothy J., additional, and Eibach, Daniel, additional

Published
2019
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46. Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame

Author

Chattaway, Marie Anne, primary, Chandra, Nastassya, additional, Painset, Anaïs, additional, Shah, Victoria, additional, Lamb, Peter, additional, Acheampong, Elsie, additional, Lo, Janice, additional, Patel, Bharat, additional, Larkin, Lesley, additional, Sergeant, Martin, additional, Cormican, Martin, additional, Litrup, Eva, additional, and Crook, Paul, additional

Published
2019
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47. Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa

Author

Ashton, Philip M, Owen, Sian V, Kaindama, Lukeki, Rowe, Will PM, Lane, Chris R, Larkin, Lesley, Nair, Satheesh, Jenkins, Claire, de Pinna, Elizabeth M, Feasey, Nicholas A, Hinton, Jay CD, and Dallman, Timothy J

Subjects
qv_600, lcsh:Genetics, lcsh:QH426-470, qu_4, qw_50, lcsh:R, lcsh:Medicine
Abstract

Background The ST313 sequence type of Salmonella Typhimurium causes invasive non-typhoidal salmonellosis and was thought to be confined to sub-Saharan Africa. Two distinct phylogenetic lineages of African ST313 have been identified. Methods We analysed the whole genome sequences of S. Typhimurium isolates from UK patients that were generated following the introduction of routine whole-genome sequencing (WGS) of Salmonella enterica by Public Health England in 2014. Results We found that 2.7% (84/3147) of S. Typhimurium from patients in England and Wales were ST313 and were associated with gastrointestinal infection. Phylogenetic analysis revealed novel diversity of ST313 that distinguished UK-linked gastrointestinal isolates from African-associated extra-intestinal isolates. The majority of genome degradation of African ST313 lineage 2 was conserved in the UK-ST313, but the African lineages carried a characteristic prophage and antibiotic resistance gene repertoire. These findings suggest that a strong selection pressure exists for certain horizontally acquired genetic elements in the African setting. One UK-isolated lineage 2 strain that probably originated in Kenya carried a chromosomally located blaCTX-M-15, demonstrating the continual evolution of this sequence type in Africa in response to widespread antibiotic usage. Conclusions The discovery of ST313 isolates responsible for gastroenteritis in the UK reveals new diversity in this important sequence type. This study highlights the power of routine WGS by public health agencies to make epidemiologically significant deductions that would be missed by conventional microbiological methods. We speculate that the niche specialisation of sub-Saharan African ST313 lineages is driven in part by the acquisition of accessory genome elements.

Published
2017

48. Multi-country outbreak of Salmonella Enteritidis phage type 8, MLVA profile 2-9-7-3-2 and 2-9-6-3-2 infections. First update, 7 March 2017

Author

Jansa, Josep, Kotila, Saara, Kramarz, Piotr, Niskanen, Taina, Palm, Daniel, Severi, Ettore, Takkinen, Johanna, Westrell, Therese, Amore, Giusi, Deserio, Domenico, Guerra, Beatriz, Hugas, Marta, Latronico, Francesca, Criado, Ernesto Liebana, Rizzi, Valentina, Bertrand, Sophie, Klamer, Sofieke, Denayer, Sarah, Mattheus, Wesley, Cantaert, Vera, Filipović, Sanja Kurečić, Rogić, Zoran, Knežević, Natalija, Petričević, Alen, Tomašić, Vlatka, Dugonjić, Zrinka, Snježana Lugarić, Humski, Andrea, Torpdahl, Mia, Müller, Luise, Silva, Nathalie Jourdan-Da, Donguy, Marie-Pierre, Hamelin, Estelle, Samain, Johanna, Hello, Simon Le, Krisztalovics, Katalin, Luzzi, Ida, Mossong, Joël, Mooijman, Kirsten, Roan Pijnacker, Franz, Eelco, Friesema, Ingrid, Leblanc, Judith, Ife Slegers-Fitz-James, Tijsma, Aloys, Brandal, Lin Thorstensen, Gołębiowska, Joanna, Kałuża, Maciej, Szewczyk, Katarzyna, Grilc, Eva, Trkov, Marija, Moa Rehn, Larkin, Lesley, Hartman, Hassan, Hawkins, Gill, Drazenka Tubin-Delic, Morgan, Deb, and Edge, Joanne

Published
2017
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50. Multi-country outbreak of Salmonella Enteritidis phage types 56 and 62, MLVA profile 2-11-3-3-2 and 2-12-3-3-2 infections

Author

Einoder-Moreno, Margot, Kotila, Saara, Palm, Daniel, Robesyn, Emmanuel, Severi, Ettore, Takkinen, Johanna, Kornschober, Christian, Mattheus, Wesley, Klamer, Sofieke, Jacquinet, Stephanie, Torpdahl, Mia, Litrup, Eva, Garvey, Patricia, McKeown, Paul, King, Joanne, Cormican, Martin, Mossong, Joël, Gras, Lapo Mughini, Franz, Eelco, Larkin, Lesley, McCormick, Jacquelyn, Dallman, Tim, and Hartman, Hassan

Published
2017
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