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1. 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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3. Molecular and Epidemiologic Analysis of Reemergent Salmonella enterica Serovar Napoli, Italy, 2011-2015

Author

Sabbatucci, Michela, Dionisi, Anna Maria, Pezzotti, Patrizio, Lucarelli, Claudia, Barco, Lisa, Mancin, Marzia, and Luzzi, Ida

Subjects
Salmonella food poisoning -- Analysis, Salmonella -- Analysis, Water resources -- Analysis, Infection -- Analysis, Food contamination -- Analysis, Vegetables -- Contamination -- Analysis, Health
Abstract

Simonella enterica serovar Napoli has attracted interest since 1982, when chocolate contaminated with this serovar and imported from Italy caused 2 foodborne outbreaks (1,2). During 2000-2006, a 140% increase in [...]

Published
2018
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6. Association of Polygenic Risk Score and Bacterial Toxins at Screening Colonoscopy with Colorectal Cancer Progression: A Multicenter Case-Control Study

Author

Piciocchi, Alfonso, primary, Germinario, Elena Angela Pia, additional, Garcia Etxebarria, Koldo, additional, Rossi, Silvia, additional, Sanchez-Mete, Lupe, additional, Porowska, Barbara, additional, Stigliano, Vittoria, additional, Trentino, Paolo, additional, Oddi, Andrea, additional, Accarpio, Fabio, additional, Grazi, Gian Luca, additional, Bruno, Giovanni, additional, Bonucci, Massimo, additional, Giambenedetti, Massimo, additional, Spigaglia, Patrizia, additional, Barbanti, Fabrizio, additional, Owczarek, Slawomir, additional, Luzzi, Ida, additional, Delibato, Elisabetta, additional, Maroccia, Zaira, additional, Nisticò, Lorenza, additional, Fiorentini, Carla, additional, D’Amato, Mauro, additional, De Angelis, Roberta, additional, and Fabbri, Alessia, additional

Published
2021
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7. Additional file 5 of Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005–2017

Author

Mastrorilli, Eleonora, Petrin, Sara, Orsini, Massimiliano, Longo, Alessandra, Cozza, Debora, Luzzi, Ida, Ricci, Antonia, Barco, Lisa, and Losasso, Carmen

Abstract

Additional file 5: Figure S3. Population recombination analysis of serovars belonging to Clade A, B, and C. Core-genome MLST (cgMLST) matrix, including 3065 alleles, trained with Salmonella enterica gene prediction model file, was used as input for STRUCTURE 2.3.3 [26]. A model-based Bayesian clustering method was used to cluster samples into groups. Samples generally clustered in accordance to the phylogenetic analysis (Fig. S2). Interestingly, in every analyzed population (K = 2 to 10), S. Napoli isolates always group together in a single population, thus highlighting that S. Napoli isolates do not show recombination with other serovars.

Published
2020
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8. Additional file 6 of Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005–2017

Author

Mastrorilli, Eleonora, Petrin, Sara, Orsini, Massimiliano, Longo, Alessandra, Cozza, Debora, Luzzi, Ida, Ricci, Antonia, Barco, Lisa, and Losasso, Carmen

Abstract

Additional file 6: Figure S4. Core genome alignement-based ML phylogeny of all genomes belonging to Clade A. core genome alignment was used for phylogenetic reconstruction using RAxML (version 7.2.8, [27]) with bootstrapping and Maximum Likelihood (ML) search under the GAMMA model of rate heterogeneity. Tree visualization was obtained using FigTree v1.4.4 [28]. S. Napoli clusters with typhoidal serovars S. Typhi and S. Paratyphi A, separately from all other non-typhoidal serovars.

Published
2020
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9. Additional file 14 of Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005–2017

Author

Mastrorilli, Eleonora, Petrin, Sara, Orsini, Massimiliano, Longo, Alessandra, Cozza, Debora, Luzzi, Ida, Ricci, Antonia, Barco, Lisa, and Losasso, Carmen

Abstract

Additional file 14: Fig.ure S8. Boxplot of detected pseudogenes distribution. Pseudogene content of S. Napoli genome was compared to two well known host-generalist serovars (S. Enteritidis and S. Typhimurium) and three host-restricted serovars (S. Typhi, S. Paratyphi A and S. Gallinarum). Both total number of identified pseudogenes (Panel A) and percentage of pseudogenes over total amount of annotated genes (Panel B) are reported. Kruskal Wallis rank sum test confirmed that a significant difference could be found in pseudogene number distribution among different serovars (p-value

Published
2020
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10. Additional file 8 of Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005–2017

Author

Mastrorilli, Eleonora, Petrin, Sara, Orsini, Massimiliano, Longo, Alessandra, Cozza, Debora, Luzzi, Ida, Ricci, Antonia, Barco, Lisa, and Losasso, Carmen

Abstract

Additional file 8 Figure S6. Bayesian phylogenetic analysis. S. Napoli STs divergence investigation was performed using BEAST [75]. The combination of strict molecular clock model and coalescent log normal population size prior was used. A mean genome-wide corrected evolutionary rate of 8.90 × 10–8 sub/site/year (credibility interval: 4.87 × 10–8, 13.10 × 10–8) was estimated starting from a 19,496 SNPs matrix built with kNP3 3.0 [71] and indicates that two ST-474 clones might have diverged around 1990. The branches of the maximum clade credibility (MCC) tree are color-coded for comparability with Fig. 2. The scale at the bottom of the tree correspond to calendar years.

Published
2020
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11. Additional file 7 of Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005–2017

Author

Mastrorilli, Eleonora, Petrin, Sara, Orsini, Massimiliano, Longo, Alessandra, Cozza, Debora, Luzzi, Ida, Ricci, Antonia, Barco, Lisa, and Losasso, Carmen

Abstract

Additional file 7 Figure S5. Core genome alignement-based ML phylogeny of S. Napoli genomes. Core genome alignment was used for phylogenetic reconstruction using RAxML (version 7.2.8, [27]) with bootstrapping and Maximum Likelihood (ML) search under the GAMMA model of rate heterogeneity. Tree visualization was obtained using FigTree v1.4.4 [28]. Within S. Napoli serovar, samples cluster primarily by ST, and divide into two major subclades. No significant correlation could be found between phylogenetic clustering and source of isolation. Here source of isolation is shown as a colour scale.

Published
2020
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12. Additional file 4 of Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005–2017

Author

Mastrorilli, Eleonora, Petrin, Sara, Orsini, Massimiliano, Longo, Alessandra, Cozza, Debora, Luzzi, Ida, Ricci, Antonia, Barco, Lisa, and Losasso, Carmen

Abstract

Additional file 4: Figure S2. Core genome alignment-based ML phylogeny of Salmonella serovars belonging to Clade A, B, and C. Core genome alignment was used for phylogenetic reconstruction kSNP3 3.0 [71], with a k-mer lenght of 21. The phylogenetic tree was derived using FastTree [72], with default parameters for nucleotide input (GTR-GAMMA model of nucleotide substitution). Subtrees were collapsed for ease of interpretation. S. Napoli clusters within Clade A, in the typhoidal subclade.

Published
2020
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18. Polymorphic DNA repair and metabolic genes: a multigenic study on gastric cancer

Author

Palli, Domenico, Polidoro, Silvia, DʼErrico, Mariarosaria, Saieva, Calogero, Guarrera, Simonetta, Calcagnile, Angelo S., Sera, Francesco, Allione, Alessandra, Gemma, Simonetta, Zanna, Ines, Filomena, Alessandro, Testai, Emanuela, Caini, Saverio, Moretti, Renato, Gomez-Miguel, Maria-Jesus, Nesi, Gabriella, Luzzi, Ida, Ottini, Laura, Masala, Giovanna, Matullo, Giuseppe, and Dogliotti, Eugenia

Published
2010
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25. 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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27. 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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38. Ascertaining the relationship between Salmonella Typhimurium and Salmonella 4,[5],12:i:- by MLVA and inferring the sources of human salmonellosis due to the two serovars in Italy

Author

Barco, Lisa, Barrucci, Federica, Cortini, Enzo, Ramon, Elena, Olsen, John Elmerdahl, Luzzi, Ida, Lettini, Antonia A, Ricci, Antonia, Barco, Lisa, Barrucci, Federica, Cortini, Enzo, Ramon, Elena, Olsen, John Elmerdahl, Luzzi, Ida, Lettini, Antonia A, and Ricci, Antonia

Abstract

The current picture of human salmonellosis shows Salmonella Typhimurium and S. 4,[5],12:i:- as the most common serovars in Italy. The aims of this study were to investigate the genetic relationship between these serovars, as well as to test the possibility of inferring sources of human salmonellosis due to S. Typhimurium and S. 4,[5],12:i:- by using multilocus variable-number tandem repeat analysis (MLVA) subtyping data. Single isolates from 268 human sporadic cases and 325 veterinary isolates (from pig, cattle, chicken, and turkey) collected over the period 2009-2011 were typed by MLVA, and the similarities of MLVA profiles were investigated using different analytical approaches. Results showed that isolates of S. 4,[5],12:i:- were more clonal compared to S. Typhimurium and that clones of both serovars from different non-human sources were very close to those which were responsible for human infections, suggesting that source attribution by MLVA typing should be possible. However, using the Asymmetric Island Model it was not possible to obtain a confident ranking of sources responsible for human infections based on MLVA profiles. The source assignments provided by the model could have been jeopardized by the high heterogeneity found within each source and the negligible divergence between sources as well as by the limited source data available, especially for some species.

Published
2015

44. An outbreak of extremely drug-resistant Pseudomonas aeruginosa in a tertiary care pediatric hospital in Italy

Author

Ciofi Degli Atti, Marta, Bernaschi, Paola, Carletti, Michaela, Luzzi, Ida, García-Fernández, Aurora, Bertaina, Alice, Sisto, Annamaria, Locatelli, Franco, Raponi, Massimiliano, Locatelli, Franco (ORCID:0000-0002-7976-3654), Ciofi Degli Atti, Marta, Bernaschi, Paola, Carletti, Michaela, Luzzi, Ida, García-Fernández, Aurora, Bertaina, Alice, Sisto, Annamaria, Locatelli, Franco, Raponi, Massimiliano, and Locatelli, Franco (ORCID:0000-0002-7976-3654)

Abstract

Background: Extensively drug-resistant Pseudomonas aeruginosa (XDR-PA) isolates are susceptible to only one or two classes of antibiotics. In 2011-2012, we investigated an outbreak of XDR-PA affecting children with onco-hematological diseases.Methods: Outbreak investigation included ascertainment of cases, tracing of intestinal carriers and environmental surveillance. Contact precautions were adopted for patients with infection or colonization. Isolates were tested for antimicrobial susceptibility; phenotypic confirmation of carbapenemase production was performed, and carbapenemase genes were tested by multiplex polymerase-chain-reaction (PCR). Genotypes were determined by pulsed-field gel electrophoresis (PFGE).Results: XDR-PA was isolated from 27 patients; 12 had bacteremia, 6 other infections and 9 were colonized. Severe neutropenia was significantly associated with bacteremia. Bloodstream-infection mortality rate was 67%. All isolates were resistant to carbapenems, cephalosporins and penicillins + beta-lactamase inhibitors. Isolates were susceptible only to colistin in 22 patients, to colistin and amikacin in 4, and to ciprofloxacin and colistin in 1. PFGE results identified 6 subtypes of a single genotype, associated with clusters of cases, and 4 sporadic genotypes. Two sporadic isolates were metallo-beta-lactamase producers, negative to PCR. All other isolates were metallo-beta-lactamase producers due to the presence of a VIM carbapenemase. Incidence of XDR-PA infections decreased from 0.72 cases/1,000 inpatient-days in March 2011-March 2012, to 0.34/1,000 in April-December 2012, after implementation of active finding of intestinal carriers on all onco-hematological inpatients.Conclusions: Control measures targeting intestinal carriers are crucial in limiting in-hospital transmission of XDR-PA polyclonal strains, protecting more vulnerable patients, such as severely neutropenic children, from developing clinical infections.

Published
2014

48. Salmonella entericaserovarTyphimurium Virulence-Resistance Plasmids Derived from the pSLT Carrying Nonconventional Class 1 Integrons withdfrA12Gene in Their Variable Region andsul3in the 3′ Conserved Segment

Author

Beutlich, Janine, primary, Rodicio, M. Rosario, additional, Mendoza, M. Carmen, additional, García, Patricia, additional, Kirchner, Miranda, additional, Luzzi, Ida, additional, Mevius, Dik, additional, Threlfall, John, additional, Helmuth, Reiner, additional, and Guerra, on behalf of the Med-Vet-Ne, Beatriz, additional

Published
2013
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49. Updated technical specifications for harmonised reporting of food-borne outbreaks through the European Union reporting system in accordance with Directive 2003/99/EC

Author

Adak, Bob, Ammon, Andrea, Chriél, Mariann, Cowden, John, Delmas, Gilles, Dierick, Katelijne, van Duynhoven, Yvonne, Hilton, Judith, Kruse, Hilde, Luzzi, Ida, Madajczak, Grzegorz, O'Flanagan, Darina, Hernandez Pezzi, Gloria, Reinecke, Annette, Werber, Dirk, Adak, Bob, Ammon, Andrea, Chriél, Mariann, Cowden, John, Delmas, Gilles, Dierick, Katelijne, van Duynhoven, Yvonne, Hilton, Judith, Kruse, Hilde, Luzzi, Ida, Madajczak, Grzegorz, O'Flanagan, Darina, Hernandez Pezzi, Gloria, Reinecke, Annette, and Werber, Dirk

Published
2011

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