92 results on '"Pongolini, S."'
Search Results
2. Detection, virulence and antimicrobial resistance of Yersinia enterocolitica in bulk tank milk in Italy
- Author
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Bonardi, S., Le Guern, A.S., Savin, C., Pupillo, G., Bolzoni, L., Cavalca, M., and Pongolini, S.
- Published
- 2018
- Full Text
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Catalog
3. Assessment of Salmonella survival in dry-cured Italian salami
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Bonardi, S., Bruini, I., Bolzoni, L., Cozzolino, P., Pierantoni, M., Brindani, F., Bellotti, P., Renzi, M., and Pongolini, S.
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- 2017
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4. Co-circulation of SARS-CoV-2 Alpha and Gamma variants in Italy, February and March 2021
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Stefanelli, P., Trentini, F., Guzzetta, G., Marziano, V., Mammone, A., Schepisi, M. S., Poletti, P., Grane, C. M., Manica, M., del Manso, M., Andrianou, X., Ajelli, M., Rezza, G., Brusaferro, S., Merler, S., Di Martino, A., Ambrosio, L., Lo Presti, A., Fiore, S., Fabiani, C., Benedetti, E., Di Mario, G., Facchini, M., Puzelli, S., Calzoletti, L., Fontana, S., Venturi, G., Fortuna, C., Marsili, G., Amendola, A., Stuppia, L., Savini, G., Picerno, A., Lopizzo, T., Dell'Edera, D., Minchella, P., Greco, F., Viglietto, G., Atripaldi, L., Limone, A., D'Agaro, P., Licastro, D., Pongolini, S., Sambri, V., Dirani, G., Zannoli, S., Affanni, P., Colucci, M. E., Capobianchi, M. R., Icardi, G., Bruzzone, B., Lillo, F., Orsi, A., Pariani, E., Baldanti, F., Molecolare, U. V., Gismondo, M. R., Maggi, F., Caruso, A., Ceriotti, F., Boniotti, M. B., Barbieri, I., Bagnarelli, P., Menzo, S., Garofalo, S., Scutella, M., Pagani, E., Collini, L., Ghisetti, V., Brossa, S., Ru, G., Bozzetta, E., Chironna, M., Parisi, A., Rubino, S., Serra, C., Piras, G., Coghe, F., Vitale, F., Tramuto, F., Scalia, G., Palermo, C. I., Mancuso, G., Pollicino, T., Di Gaudio, F., Vullo, S., Reale, S., Cusi, M. G., Rossolini, G. M., Pistello, M., Mencacci, A., Camilloni, B., Severini, S., Di Benedetto, M., Terregino, C., Monne, I., Biscaro, V., Stefanelli P, Trentini F, Guzzetta G, Marziano V, Mammone A, Sane Schepisi M, Poletti P, Molina Grané C, Manica M, Del Manso M, Andrianou X, Ajelli M, Rezza G, Brusaferro S, Merler S, Vitale F, Tramuto F, Stefanelli P., Trentini F., Guzzetta G., Marziano V., Mammone A., Sane Schepisi M., Poletti P., Molina Grane C., Manica M., Del Manso M., Andrianou X., Ajelli M., Rezza G., Brusaferro S., Merler S., Sambri V, and (membro del COVID-19 National Microbiology Surveillance Study Group) more...
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Epidemiology ,SARS-CoV-2 ,Public Health, Environmental and Occupational Health ,COVID-19 ,co-circulation ,lineage ,SARS-CoV-2 variant of concern ,transmissibility ,Humans ,Italy ,Models, Theoretical ,Settore MED/42 - Igiene Generale E Applicata ,SARS-COV-2 VARIANT OF CONCERN, CO-CIRCULATION, LINEAGE, TRANSMISSIBILITY, HUMANS, ITALY, MODELS, THEORETICAL, COVID-19, SARS-COV-2 ,Theoretical ,Models ,Virology ,Human - Abstract
Background Several SARS-CoV-2 variants of concern (VOC) have emerged through 2020 and 2021. There is need for tools to estimate the relative transmissibility of emerging variants of SARS-CoV-2 with respect to circulating strains. Aim We aimed to assess the prevalence of co-circulating VOC in Italy and estimate their relative transmissibility. Methods We conducted two genomic surveillance surveys on 18 February and 18 March 2021 across the whole Italian territory covering 3,243 clinical samples and developed a mathematical model that describes the dynamics of co-circulating strains. Results The Alpha variant was already dominant on 18 February in a majority of regions/autonomous provinces (national prevalence: 54%) and almost completely replaced historical lineages by 18 March (dominant across Italy, national prevalence: 86%). We found a substantial proportion of the Gamma variant on 18 February, almost exclusively in central Italy (prevalence: 19%), which remained similar on 18 March. Nationally, the mean relative transmissibility of Alpha ranged at 1.55–1.57 times the level of historical lineages (95% CrI: 1.45–1.66). The relative transmissibility of Gamma varied according to the assumed degree of cross-protection from infection with other lineages and ranged from 1.12 (95% CrI: 1.03–1.23) with complete immune evasion to 1.39 (95% CrI: 1.26–1.56) for complete cross-protection. Conclusion We assessed the relative advantage of competing viral strains, using a mathematical model assuming different degrees of cross-protection. We found substantial co-circulation of Alpha and Gamma in Italy. Gamma was not able to outcompete Alpha, probably because of its lower transmissibility. more...
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- 2022
5. Transmission patterns of a Mycobacterium avium subsp. paratuberculosis clone within a single heard investigated by Whole Genome Sequencing
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Bolzoni, L., primary, Scaltriti, E., additional, Russo, S., additional, Pongolini, S., additional, Garbarino, C., additional, Leo, S., additional, Arrigoni, N., additional, and Ricchi, M., additional
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- 2021
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6. Risk identification in food safety: Strategy and outcomes of the EFSA emerging risks exchange network (EREN), 2010–2014
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Costa, M.C., Goumperis, T., Andersson, W., Badiola, J., Ooms, W., Pongolini, S., Saegerman, C., Jurkovic, M., Tuominen, P., Tsigarida, E., Steinwider, J., Hölzl, C., Mikushinska, N., Gross-Bošković, A., Kanari, P., Christodoulidou, M., Babička, L., Korsgaard, H., Pesonen, S., Fillet, A.M., Foures, F., Lohman, M., Luber, P., Szabó, M., Cseh, J., Noteborn, H.P.J.M., Færden, K., Fulke, Å., Trnovec, T., Ilbäck, N.G., Andersson, T., Donohoe, T., Merten, C., and Robinson, T. more...
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- 2017
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7. Genomic epidemiology of Klebsiella pneumoniae: the Italian scenario, and novel insights into the origin and global evolution of resistance to carbapenem antibiotics
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Gaiarsa, S., Comandatore, F., Corbella, M., Valle, C. D., Epis, S., Scaltriti, E., Carretto, E., Farina, C., Labonia, M., Pongolini, S., Bandi, C., Marone, P., Sassera, D., GAIBANI, PAOLO, LANDINI, MARIA PAOLA, SAMBRI, VITTORIO, Gaiarsa, S., Comandatore, F., Gaibani, P., Corbella, M., Valle, C. D., Epis, S., Scaltriti, E., Carretto, E., Farina, C., Labonia, M., Landini, M. P., Pongolini, S., Sambri, V., Bandi, C., Marone, P., and Sassera, D. more...
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Klebsiella pneumoniae, antimicrobial resistance ,carbapenemases, Italy ,genomic epidemiology - Abstract
Klebsiella pneumoniae is at the forefront of antimicrobial resistance for Gram-negative pathogenic bacteria, as strains resistant to third-generation cephalosporins and carbapenems are widely reported. The worldwide diffusion of these strains is of great concern, also due to the high morbidity and mortality often associated with K. pneumoniae infections in nosocomial environments. We sequenced the genomes of 89 K. pneumoniae strains, isolated in six Italian hospitals. Strains were selected based on antibiotypes, regardless of multilocus sequence type, to obtain a picture of the epidemiology of K. pneumoniae in Italy. Thirty-one strains were carbapenem-resistant K. pneumoniae carbapenemase producers; 29 were resistant to third-generation cephalosporins; 29 were susceptible to the aforementioned antibiotics. The genomes were compared with all the sequences available in the databases, obtaining a dataset of 319 genomes spanning the known diversity of K. pneumoniae worldwide. Bioinformatic analyses of this global dataset allowed us to construct a whole-species phylogeny, to detect patterns of antibiotic resistance distribution, and to date the differentiation between specific clades of interest. Finally we detected a ∼1.3 Mb recombination that characterizes all the isolates of Clonal Complex 258, the most widespread carbapenem-resistant group of K. pneumoniae. The evolution of this complex was modelled, dating the newly detected and the previously reported recombination events. The present study contributes to the understanding of K. pneumoniae evolution, providing novel insights into its global genomic characteristics, and drawing a dated epidemiological scenario for this pathogen in Italy. more...
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- 2014
8. Occurrence of Vibrio spp. in shellfish harvested from Emilia Romagna coast (North-western Adriatic Sea, Italy)
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Rubini S., Losio M. N., Pavoni E., Bianchi L., Galletti G., Scordella G., Bresolin R., Pongolini S., PIANO, ANNAMARIA, SERRATORE, PATRIZIA, Rubini S., Losio M.N., Pavoni E., Bianchi L., Galletti G., Scordella G., Bresolin R., Pongolini S., Piano A., and Serratore P. more...
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- 2009
9. The associations between animal-based welfare measures and the presence of indicators of food safety in finishing pigs
- Author
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Alpigiani, I, primary, Bacci, C, additional, Keeling, LJ, additional, Salman, MD, additional, Brindani, F, additional, Pongolini, S, additional, Hitchens, PL, additional, and Bonardi, S, additional
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- 2016
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10. Survey on the presence of Mycobacterium avium subsp. paratuberculosis in ground beef from an industrial meat plant
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Savi, R., primary, Ricchi, M., additional, Cammi, G., additional, Garbarino, C., additional, Leo, S., additional, Pongolini, S., additional, and Arrigoni, N., additional
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- 2015
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11. On line objective evaluation of pork quality
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Chizzolini, R., Delbono, G., Novelli, Enrico, Pongolini, S., and Rosa, P.
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- 1991
12. A new marker protein in the nose
- Author
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BIGNETTI, E, primary, RAMONI, R, additional, GROLLI, S, additional, and PONGOLINI, S, additional
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- 1990
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13. Reduction trend of mcr-1 circulation in Emilia-Romagna Region, Italy
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Simone Ambretti, Chiara Bracchi, Vittorio Sambri, Carlo Biagetti, Adriana Calderaro, Claudia Venturelli, Giuseppe Diegoli, Ilaria Menozzi, Maria Federica Pedna, Martina Tambassi, Rossella Buttazzi, Carlo Gagliotti, Stefano Pongolini, Mario Sarti, Enrico Ricchizzi, Marianna Meschiari, Maria Luisa Moro, Erika Scaltriti, Massimo Confalonieri, Agostino Barozzi, Marina Morganti, Laura Soliani, Roberta Schiavo, Edoardo Carretto, Luca Bolzoni, Fabio Tumietto, Chiara Casadio, Gagliotti C., Bolzoni L., Carretto E., Sarti M., Ricchizzi E., Ambretti S., Barozzi A., Bracchi C., Confalonieri M., Menozzi I., Morganti M., Pedna M.F., Sambri V., Scaltriti E., Schiavo R., Soliani L., Tambassi M., Venturelli C., Biagetti C., Buttazzi R., Calderaro A., Casadio C., Meschiari M., Tumietto F., Diegoli G., Pongolini S., and Moro M.L. more...
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Microbiology (medical) ,Veterinary medicine ,Antimicrobials for veterinary use ,Antibiotic resistance ,Clonal dissemination ,Klebsiella pneumoniae ,Population ,Drug Resistance ,Horizontal transfer ,Bacterial Protein ,Microbial Sensitivity Tests ,Minimum inhibitory concentration ,Enterobacterales ,One Health approach ,Plasmid ,Bacterial Proteins ,Enterobacteriaceae ,Enterobacterale ,Anti-Bacterial Agent ,Drug Resistance, Bacterial ,medicine ,Humans ,Colistin ,Mcr ,Anti-Bacterial Agents ,Enterobacteriaceae Infections ,Ethanolaminephosphotransferase ,Italy ,Phylogeny ,Retrospective Studies ,education ,education.field_of_study ,biology ,Microbial Sensitivity Test ,Bacterial ,General Medicine ,biology.organism_classification ,Enterobacteriaceae Infection ,Infectious Diseases ,Salmonella enterica ,MCR-1 ,Enterobacter cloacae ,hormones, hormone substitutes, and hormone antagonists ,Human ,medicine.drug - Abstract
This study aims to describe trends of mcr-positive Enterobacterales in humans based on laboratory surveillance with a defined catchment population. The data source is the Micro-RER surveillance system, established in Emilia-Romagna region (Italy), to monitor the trend of mcr resistance. Enterobacterales isolates from human clinical samples with minimum inhibitory concentration (MIC) ≥ 2mg/L for colistin were sent to the study reference laboratory for the detection of mcr genes. Isolates prospectively collected in the period 2018–2020 were considered for the assessment of population rates and trends; further analyses were carried out for the evaluation of clonality and horizontal mcr gene transfer. Previous isolates from local laboratory collection were also described. In the period 2018–2020, 1164 isolates were sent to the reference laboratory, and 51 (4.4%) were confirmed as mcr-positive: 50 mcr-1 (42 Escherichia coli, 6 Klebsiella pneumoniae, 2 Salmonella enterica) and 1 mcr-4 (Enterobacter cloacae). The number of mcr-positive isolates dropped from 24 in the first half of 2018 to 3 in the whole of 2020 (trend p value < 0.001). Genomic analyses showed the predominant role of the horizontal transfer of mcr genes through plasmids or dissemination of transposable elements compared to clonal dissemination of mcr-positive microorganisms. The study results demonstrate a substantial decrease in the circulation of mcr-1 plasmid genes in Emilia-Romagna Region. more...
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- 2021
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14. Salmonella spp. prevalence, pattern of spread and transmission in foals and mares hospitalized at an equine perinatology unit
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ZACCARIA, ANDREA CHIARA, MARIELLA, JOLE, FRECCERO, FRANCESCA, PONGOLINI, STEFANO, CINOTTI, STEFANO, CASTAGNETTI, CAROLINA, Merialdi, G, D’Incau, M, Zaccaria, AC, Mariella, J, Freccero, F, Merialdi, G, Pongolini, S, D’Incau, M, Cinotti, S, and Castagnetti, C. more...
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Salmonella, foal, trasmission - Published
- 2016
15. First report of an Enterobacter cloacae ST837 resistant to cefiderocol co-harbouring bla IMP-19 and mcr 4.3 resistance genes, in Italy.
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Menozzi I, Scaltriti E, Secci B, Dodi A, Lazzarotto T, Pongolini S, Foschi C, and Ambretti S
- Abstract
Objectives: We described the molecular characterization of an Enterobacter cloacae strain resistant to cefiderocol, co-harbouring bla
IMP-19 and mcr-4.3 resistance genes METHODS: The strain was isolated from the rectal swab of a 77-year-old woman during the screening for the detection of patients colonized by carbapenemase-producing Enterobacterales (CPE), in Bologna (Italy). The strain was identified at the species level by MALDI-TOF mass spectrometry and the presence of IMP carbapenemase was confirmed both by a phenotypic immunochromatographic method, and by a rapid commercial NAAT. The strain underwent an antimicrobial susceptibility testing and its genome was fully characterized to assess (i) the Multi Locus Sequence Type (MLST), (ii) the presence of antimicrobial resistance genes (AMR), (iii) the presence of virulence genes coupled with Mobile Genetic Elements., Results: MLST identified the strain as ST837. A plasmid of 60'691 bp, very similar to MW574937 plasmid of Escherichia coli was identified and carried the following AMR genes: aac(6')-II,blaBEL-1 , blaIMP-19 , msr(E), mph(E), sul1. This plasmid harboured several tra gene (traB, traC, traD, traG, traI, traJ, traKtraL, traM) of the transfer operon of E. coli conjugative F plasmid. Other AMR genes were located in the chromosome (blaCMH-3 and fosA) or in other plasmids (blaSHV-12 and mcr-4.3). In vitro the strain showed resistance to many beta-lactams, including cefiderocol, whereas, despite the presence of mcr-4.3 gene, it was susceptible to colistin., Conclusions: Further studies are needed to better evaluate the origin of this strain, monitoring the presence of gram-negative bacilli with a similar molecular structure in our area., Competing Interests: Declaration of competing interest None declared., (Copyright © 2025. Published by Elsevier Ltd.) more...- Published
- 2025
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16. Outbreak of carbapenem resistant Klebsiella pneumoniae in a neurorehabilitation unit: Genomic epidemiology reveals complex transmission pattern in a tertiary care hospital.
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Silvotti MG, Scaltriti E, Bolzoni L, Zerbi B, Tocci G, Zappavigna A, Lamberti G, Donati F, Federici F, Pongolini S, and Lo Cascio G
- Abstract
Objectives: Infections by carbapenem-resistant Enterobacterales (CRE) in hospitals represent a severe threat but little is known on outbreaks in rehabilitation wards caused by Klebsiella pneumoniae producing Klebsiella pneumoniae Carbapenemase (KPC-Kp). We report an outbreak by KPC-Kp, in a neurorehabilitation unit in Italy, analysed through whole-genome sequencing (WGS) for transmission routes reconstruction to improve management of KPC-Kp infections in rehabilitation units., Methods: We investigated cases and KPC-Kp isolates collected from February to October 2022 from hospital surveillance. Carbapenem resistance was identified with disk diffusion and minimum inhibitory concentration tests, carbapenemase production through immunochromatographic lateral flow assays. All isolates were genotyped through WGS to highlight possible phylogenetic relationships. The most likely transmission networks of KPC-Kp were reconstructed with Bayesian discrete-time stochastic models., Results: Nineteen patients were colonized by KPC-Kp. Two isolates belonged to sporadic sequence types (STs; ST348 and ST219) whereas 9 of 19 and 8 of 19 isolates belonged to ST307 and ST716, respectively. Among the ST307 isolates, we identified two genomically distinct clusters of five and two cases. All ST716 isolates were highly similar. Genotyping and the reconstruction of transmission networks of KPC-Kp based on genomic data identified seven independent introductions into the neurorehabilitation unit rather than a single outbreak as initially hypothesized before genomic investigation. Three of the seven introductions generated chains of secondary infections, whereas the remaining four remained single cases., Conclusions: The outbreak root-causes were identified in temporary staff shortage and insufficient microbiological surveillance. Measures were adopted accordingly and the outbreak ended. The study highlights the critical role of genomic epidemiology in hospital outbreaks. © 2025 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy., (Copyright © 2025 The Authors. Published by Elsevier Ltd.. All rights reserved.) more...
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- 2025
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17. Outbreak of Salmonella enterica subsp. enterica Serovar Napoli on a Dairy Cow Farm.
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Ricchi M, Filippi A, Scaltriti E, Tambassi M, Pongolini S, Bolzoni L, Prosperi A, Torreggiani C, Cammi M, Chiatante A, Arrigoni N, Massella E, Luppi A, and Garbarino C
- Abstract
Salmonella is diffused worldwide, and Salmonella enterica subsp. enterica is spread worldwide with many serovars associated with the infection of domestic bovines. The most spread are S . Dublin, S . Typhimurium and S . Infantis. S. Napoli is, however very rarely reported in domestic ruminants. Here, we report an outbreak of S . Napoli on a dairy cow farm in Northern Italy (Piacenza). A total of 18 S . Napoli isolates were recovered from aborted fetuses, feces, tissues and environmental samples. Whole genome sequencing suggested that all isolates belonged to the same cluster. After the application of stringent biocontainment and biosecurity measures, no further cases were reported. However, four months after the first case, the serovar was still isolated in environmental samples, underlying the importance of adopting the correct biosecurity and biocontainment measures in order to prevent the circulation and transmission of Salmonella within the farm. more...
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- 2025
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18. Salmonella pathogenicity Island 1 undergoes decay in serovars adapted to swine and poultry.
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Tambassi M, Berni M, Bracchi C, Menozzi I, Dodi A, Mazzera L, Morganti M, Scaltriti E, and Pongolini S
- Abstract
Human salmonellosis is a high-priority foodborne disease worldwide. The main reservoir of Salmonella is livestock, mainly swine and poultry that are infected both by generalist serovars and serovars adapted to them. The most widespread livestock-adapted serovars are attenuated in both their primary hosts and humans. We previously identified a lineage of the swine-adapted Salmonella Derby carrying mutations in Salmonella Pathogenicity Island-1(SPI-1) giving attenuation. To evaluate if SPI-1 decay is a general feature of swine-adapted serovars, we analyzed the Enterobase global population of Salmonella serovars most frequently isolated from swine. We found that deleterious mutations in SPI-1 are accumulated more in swine-adapted ( S . Derby and Salmonella Rissen) than in generalist ( Salmonella Typhimurium, I 1,4,[5],12:i:-, and Salmonella Infantis) serovars. The genomes carrying such mutations are widespread in the population of S . Derby and S . Rissen, indicating that the occurrence and fixation of deleterious mutations in SPI-1 are frequent. Similarly, also poultry-adapted Salmonella Kentucky has accumulated deleterious mutations in SPI-1, leading to over 70% of mutated genomes of this serovar compared with negligible proportions of mutated genomes in the generalist serovars from poultry. Although in vitro attenuation of S . Derby carrying mutated SPI-1 had been previously demonstrated, we showed the same phenotype for mutated S . Rissen. Considering also the known attenuation of S . Kentucky, our population-scale findings provide evidence of progressive evolution toward the attenuation of serovars adapted to the main animal reservoirs of human salmonellosis through the food chain. Intensive farming with a high density of animals could be a possible driver of this evolution.IMPORTANCEThis study shows at the global population level of Salmonella that the main attenuated serovars adapted to food-producing animals are undergoing convergent evolution toward further attenuation through the decay of SPI-1, considered critically important for the intestinal phase of Salmonella infection. The drivers of this evolution are unknown, but they could be attributed, at least in part, to the intensive farming of livestock with its high densities. On one side, our results contribute to the knowledge of the interaction between livestock populations and their host-adapted serovars of Salmonella . On the other side, the study provides scientific background for reconsidering the microbiological criteria adopted by the food safety legislation of many countries that ask for the absence of Salmonella in foods, regardless of any virulence evaluation of the detected strain. In this respect, the study provides molecular bases to investigate the virulence of different lineages within these host-adapted serovars. more...
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- 2024
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19. Concanavalin A Delivers a Photoactive Protein to the Bacterial Wall.
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Mussini A, Delcanale P, Berni M, Pongolini S, Jordà-Redondo M, Agut M, Steinbach PJ, Nonell S, Abbruzzetti S, and Viappiani C
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- Streptavidin chemistry, Streptavidin metabolism, Bacterial Proteins metabolism, Protein Binding, Concanavalin A chemistry, Concanavalin A metabolism, Escherichia coli metabolism, Staphylococcus aureus metabolism, Cell Wall metabolism
- Abstract
Modular supramolecular complexes, where different proteins are assembled to gather targeting capability and photofunctional properties within the same structures, are of special interest for bacterial photodynamic inactivation, given their inherent biocompatibility and flexibility. We have recently proposed one such structure, exploiting the tetrameric bacterial protein streptavidin as the main building block, to target S. aureus protein A. To expand the palette of targets, we have linked biotinylated Concanavalin A, a sugar-binding protein, to a methylene blue-labelled streptavidin. By applying a combination of spectroscopy and microscopy, we demonstrate the binding of Concanavalin A to the walls of Gram-positive S. aureus and Gram-negative E. coli . Photoinactivation is observed for both bacterial strains in the low micromolar range, although the moderate affinity for the molecular targets and the low singlet oxygen yields limit the overall efficiency. Finally, we apply a maximum entropy method to the analysis of autocorrelation traces, which proves particularly useful when interpreting signals measured for diffusing systems heterogeneous in size, such as fluorescent species bound to bacteria. more...
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- 2024
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20. Salmonella in horses at slaughter and public health effects in Italy.
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Bolzoni L, Conter M, Lamperti L, Scaltriti E, Morganti M, Poeta A, Vecchi M, Paglioli S, Rampini A, Ramoni P, De Vita D, Bacci C, Rega M, Andriani L, Pongolini S, and Bonardi S
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- Humans, Horses, Animals, Public Health, Multilocus Sequence Typing, Salmonella enteritidis, Italy epidemiology, Meat, Salmonella Food Poisoning epidemiology, Salmonella enterica, Asteraceae
- Abstract
The study assessed the role of equids at slaughter as faecal carriers of Salmonella enterica and the occurrence of contaminated equid carcasses during the slaughter process in Northern Italy (Emilia-Romagna Region). From June to November 2021, 152 equids (146 horses, 5 donkeys and 1 mule) were tested for Salmonella both in caecal contents and through carcass swabs. Antimicrobial resistance (AMR) of recovered strains was tested against 15 antimicrobials. Salmonella was detected in 3/152 of the caecal contents (2.0 %), while all carcass samples were negative. S. enterica serovars Enteriditis, Typhimurium and Stanleyville were identified. The only AMR isolate was S. Typhimurium with AMR profile AmCStxT. Considering the consumption of raw horse meat (i.e., minced raw meat named "pesto di cavallo" and dried and smoked strips named "sfilacci di cavallo") in different areas of Northern Italy, we also investigated the possible link between horse meat eating and salmonellosis cases in the human population in the same area. Specifically, we compared the Salmonella strains collected during the study with those routinely processed in the laboratory surveillance system for human salmonellosis in Emilia-Romagna (a region with about 4.5 million inhabitants). The comparison was based on whole genome sequencing data through core genome multi-locus sequence typing (cgMLST) used in routine surveillance. A genomic match in cgMLST was found between the strain of S. enterica serovar Enteritidis isolated from a horse caecal content and an enduring outbreak of 17 human cases in Emilia-Romagna during the study period. The consequent epidemiological investigation highlighted that a number of cases with known food history reported the consumption of horse meat and traced different batches of the consumed meat, released weeks apart from each other, to the slaughter investigated in the study. The results of the epidemiological investigation suggested the role of horses in the S. enterica serovar Enteritidis outbreak affecting raw horse meat consumers. This study shows that, despite the low prevalence on equid carcasses, S. enterica in horse meat can represent a risk to consumers. From the perspective of the slaughter activities, this highlights the need to maintain a high level of hygiene during the entire process, starting from the hygiene at lairage up to the slaughtering phase and dressing of carcasses., Competing Interests: Declaration of competing interest None., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.) more...
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- 2024
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21. Salmonella Derby adaptation to swine and simultaneous attenuation for humans go through decay of Salmonella Pathogenicity Island I.
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Berni M, Bolzoni L, Menozzi I, Dodi A, Bracchi C, Morganti M, Scaltriti E, Pongolini S, and Tambassi M
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- Humans, Animals, Swine, Salmonella genetics, Phenotype, Bacterial Proteins genetics, Genomic Islands, Salmonella enterica genetics
- Abstract
Importance: This study integrated population data with in vitro assessment of virulence phenotypes to unveil that a considerable part of the global population of Salmonella Derby is evolving to enhance its host adaptation to the swine host and that this evolution is simultaneously increasing its attenuation for humans. The study shows that the fixation of deleterious mutations in SPI-1 has a role in this process. This evidence indicates that SPI-1 has a key role for S . Derby virulence in humans but not for its circulation in swine. The results show that genes generally considered essential for Salmonella pathogenesis do not play the same key role for all Salmonella serovars or lineages and/or all hosts. The study helps in understanding the molecular mechanisms underlying the ecology and host adaptation of Salmonella showing that the adaptation process can vary for different types of Salmonella and hosts., Competing Interests: The authors declare no conflict of interest. more...
- Published
- 2023
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22. Listeria monocytogenes Transmission from Donated Blood to Platelet Transfusion Recipient, Italy.
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Gori M, Bolzoni L, Scaltriti E, Andriani L, Marano V, Morabito F, Fappani C, Cereda D, Giompapa E, Chianese R, Lanzini P, Martinelli LA, Bianchi S, Amendola A, Pongolini S, and Tanzi E
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- Humans, Blood Platelets, Platelet Transfusion adverse effects, Italy epidemiology, Food Microbiology, Listeria monocytogenes genetics, Listeriosis microbiology
- Abstract
We report Listeria monocytogenes infection in a patient in Italy who was transfused with pooled platelet concentrate. Genomic analysis revealed that L. monocytogenes isolates from the donor blood unit, the transfused platelets, and the patient's blood culture were genetically closely related, confirming transfusion transmission. Additional surveillance and secondary bacterial screening could improve transfusion safety. more...
- Published
- 2023
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23. A Fatal Case of Pseudomonas aeruginosa Community-Acquired Pneumonia in an Immunocompetent Patient: Clinical and Molecular Characterization and Literature Review.
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Barp N, Marcacci M, Biagioni E, Serio L, Busani S, Ventura P, Franceschini E, Orlando G, Venturelli C, Menozzi I, Tambassi M, Scaltriti E, Pongolini S, Sarti M, Pietrangelo A, Girardis M, Mussini C, and Meschiari M more...
- Abstract
Rare cases of Pseudomonas aeruginosa community-acquired pneumonia (PA-CAP) were reported in non-immunocompromised patients. We describe a case of Pseudomonas aeruginosa (PA) necrotizing cavitary CAP with a fatal outcome in a 53-year-old man previously infected with SARS-CoV-2, who was admitted for dyspnea, fever, cough, hemoptysis, acute respiratory failure and a right upper lobe opacification. Six hours after admission, despite effective antibiotic therapy, he experienced multi-organ failure and died. Autopsy confirmed necrotizing pneumonia with alveolar hemorrhage. Blood and bronchoalveolar lavage cultures were positive for PA serotype O:9 belonging to ST1184. The strain shares the same virulence factor profile with reference genome PA01. With the aim to better investigate the clinical and molecular characteristics of PA-CAP, we considered the literature of the last 13 years concerning this topic. The prevalence of hospitalized PA-CAP is about 4% and has a mortality rate of 33-66%. Smoking, alcohol abuse and contaminated fluid exposure were the recognized risk factors; most cases presented the same symptoms described above and needed intensive care. Co-infection of PA-influenza A is described, which is possibly caused by influenza-inducing respiratory epithelial cell dysfunction: the same pathophysiological mechanism could be assumed with SARS-CoV-2 infection. Considering the high rate of fatal outcomes, additional studies are needed to identify sources of infections and new risk factors, along with genetic and immunological features. Current CAP guidelines should be revised in light of these results. more...
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- 2023
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24. Klebsiella pneumoniae carrying multiple alleles of antigen 43-encoding gene of Escherichia coli associated with biofilm formation.
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Tambassi M, Passarini E, Menozzi I, Berni M, Bracchi C, Dodi A, Bolzoni L, Scaltriti E, Morganti M, Ferrarini G, Sordi L, Sarti M, Ambretti S, and Pongolini S
- Subjects
- Alleles, Anti-Bacterial Agents, Antigens, Bacterial genetics, Biofilms, Colistin, Escherichia coli genetics, Microbial Sensitivity Tests, Plasmids genetics, Escherichia coli Proteins genetics, Klebsiella pneumoniae genetics
- Abstract
A clinical strain of Klebsiella pneumoniae typed as sequence type 307 carrying three different alleles of the flu gene encoding the Escherichia coli virulence factor antigen 43 associated with biofilm formation was detected and characterized. The flu alleles are located in the chromosome inside putative integrative conjugative elements. The strain displays the phenotypes associated with Ag43, i.e. bi-phasic colony morphology and enhanced biofilm production. Furthermore, the strain produces low amount of capsule known to affect Ag43 function. Analysis of 1431 worldwide deposited genomes revealed that 3.7% Klebsiella pneumoniae carry one or two flu alleles., (© 2023. The Author(s).) more...
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- 2023
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25. Different Roles of Wild Boars and Livestock in Salmonella Transmission to Humans in Italy.
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Bolzoni L, Bonardi S, Tansini C, Scaltriti E, Menozzi I, Morganti M, Conter M, and Pongolini S
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- Humans, Animals, Cattle, Swine, Salmonella genetics, Animals, Wild, Poultry, Sus scrofa, Livestock, Salmonella Infections, Animal epidemiology
- Abstract
Wild boar (Sus scrofa) is the most widely distributed large wildlife mammal worldwide. To investigate the transmission of Salmonella enterica amongst wild boars (Sus scrofa), humans, and livestock, we compared via pulsed-field gel electrophoresis and whole genome sequences the isolates of S. enterica serovar Typhimurium (biphasic and monophasic variants) and Enteritidis collected from wild boars, food-producing animals, and human patients in Emilia-Romagna region (Northern Italy) between 2017 and 2020. Specifically, we analysed 2175 isolates originated from human (1832), swine (117), bovine (128), poultry (76), and wild boar (22). The genomic analyses showed that wild boars shared most of their lineages of biphasic Typhimurium with bovines and most of Enteritidis with poultry, whilst we did not find any lineage shared with swine. Moreover, almost 17% of human biphasic Typhimurium and Enteritidis belonged to genomic clusters including wild boar isolates, but the inclusion of bovine and poultry isolates in the same clusters and the peculiar spatial distribution of the isolates suggested that human cases (and wild boar infections) likely originated from bovines and poultry. Consequently, wild boars appear not to play a significant role in infecting humans with these serovars, but seem to get infected themselves from livestock, probably through the environment., (© 2023. EcoHealth Alliance.) more...
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- 2023
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26. Machine learning-based typing of Salmonella enterica O-serogroups by the Fourier-Transform Infrared (FTIR) Spectroscopy-based IR Biotyper system.
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Cordovana M, Mauder N, Join-Lambert O, Gravey F, LeHello S, Auzou M, Pitti M, Zoppi S, Buhl M, Steinmann J, Frickmann H, Dekker D, Funashima Y, Nagasawa Z, Soki J, Orosz L, Veloo AC, Justesen US, Holt HM, Liberatore A, Ambretti S, Pongolini S, Soliani L, Wille A, Rojak S, Hagen RM, May J, Pranada AB, and Kostrzewa M more...
- Subjects
- Agar, Artificial Intelligence, Bacterial Typing Techniques methods, Culture Media, Ethanol, Humans, Machine Learning, Salmonella, Serogroup, Spectroscopy, Fourier Transform Infrared methods, Water, Salmonella enterica
- Abstract
Background: Salmonella enterica is among the major burdens for public health at global level. Typing of salmonellae below the species level is fundamental for different purposes, but traditional methods are expensive, technically demanding, and time-consuming, and therefore limited to reference centers. Fourier transform infrared (FTIR) spectroscopy is an alternative method for bacterial typing, successfully applied for classification at different infra-species levels., Aim: This study aimed to address the challenge of subtyping Salmonella enterica at O-serogroup level by using FTIR spectroscopy. We applied machine learning to develop a novel approach for S. enterica typing, using the FTIR-based IR Biotyper® system (IRBT; Bruker Daltonics GmbH & Co. KG, Germany). We investigated a multicentric collection of isolates, and we compared the novel approach with classical serotyping-based and molecular methods., Methods: A total of 958 well characterized Salmonella isolates (25 serogroups, 138 serovars), collected in 11 different centers (in Europe and Japan), from clinical, environmental and food samples were included in this study and analyzed by IRBT. Infrared absorption spectra were acquired from water-ethanol bacterial suspensions, from culture isolates grown on seven different agar media. In the first part of the study, the discriminatory potential of the IRBT system was evaluated by comparison with reference typing method/s. In the second part of the study, the artificial intelligence capabilities of the IRBT software were applied to develop a classifier for Salmonella isolates at serogroup level. Different machine learning algorithms were investigated (artificial neural networks and support vector machine). A subset of 88 pre-characterized isolates (corresponding to 25 serogroups and 53 serovars) were included in the training set. The remaining 870 samples were used as validation set. The classifiers were evaluated in terms of accuracy, error rate and failed classification rate., Results: The classifier that provided the highest accuracy in the cross-validation was selected to be tested with four external testing sets. Considering all the testing sites, accuracy ranged from 97.0% to 99.2% for non-selective media, and from 94.7% to 96.4% for selective media., Conclusions: The IRBT system proved to be a very promising, user-friendly, and cost-effective tool for Salmonella typing at serogroup level. The application of machine learning algorithms proved to enable a novel approach for typing, which relies on automated analysis and result interpretation, and it is therefore free of potential human biases. The system demonstrated a high robustness and adaptability to routine workflows, without the need of highly trained personnel, and proving to be suitable to be applied with isolates grown on different agar media, both selective and unselective. Further tests with currently circulating clinical, food and environmental isolates would be necessary before implementing it as a potentially stand-alone standard method for routine use., Competing Interests: Declaration of Competing Interest O.J.L, F.G., S.L., M.A., M.P., S.Z., M.B., J.S., H.F., D.D., Y.F., Z.N., J.S., L.O., A.C.V., U.S.J., H.M.H., A.L., S.A., S.P., L.S., A.W., S.R., R.M.H., J.M. and A.B.P. declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. M.C., N.M. and M.K. are Bruker's employees., (Copyright © 2022 Elsevier B.V. All rights reserved.) more...
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- 2022
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27. Comparative analysis of two genomes of Chlamydia pecorum isolates from an Alpine chamois and a water buffalo.
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Rigamonti S, Floriano AM, Scaltriti E, Longbottom D, Livingstone M, Comandatore F, Pongolini S, Capucci L, Mandola ML, Bazzucchi M, Prati P, and Vicari N
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- Animals, Buffaloes, Chlamydia, Chlamydia trachomatis, Tryptophan metabolism, Rupicapra metabolism
- Abstract
Background: To date, whole genome sequencing has been performed mainly for isolates of Chlamydia trachomatis, C. pneumoniae, C. psittaci and C. abortus, but only a few isolates of C. pecorum have been entirely sequenced and this makes it difficult to understand its diversity and population structure. In this study the genome of two C. pecorum strains isolated from the lung of an Alpine chamois affected with pneumonia (isolate PV7855) and the brain of a water buffalo affected with meningoencephalomyelitis (isolate PV6959), were completely sequenced with MiSeq system (Illumina) and analyzed in their most polymorphic regions., Results: The genome length and GC content of the two isolates were found to be consistent with other C. pecorum isolates and the gene content of polymorphic membrane proteins and plasticity zone was found to be very similar. Some differences were observed in the phospholipase genes for both isolates and in the number of genes in the plasticity zone, such as the presence of some hypothetical proteins in PV6959, not present in any other genomes analyzed in this study. Interestingly, PV6959 possesses an extra pmp and has an incomplete tryptophan biosynthesis operon. Plasmids were detected in both isolates., Conclusions: Genome sequencing of the two C. pecorum strains did not reveal differences in length and GC content despite the origin from different animal species with different clinical disease. In the plasticity zone, the differences in the genes pattern might be related to the onset of specific symptoms or infection of specific hosts. The absence of a tryptophan biosynthesis pathway in PV6959 may suggest a strict relationship between C. pecorum and its host., (© 2022. The Author(s).) more...
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- 2022
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28. Automated Analysis of Intracellular Phenotypes of Salmonella using ImageJ.
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Berni M, Pongolini S, and Tambassi M
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- Cytosol metabolism, Epithelial Cells metabolism, Phenotype, Salmonella typhimurium genetics, Vacuoles microbiology
- Abstract
Salmonella is an enteric pathogen able to invade the intestinal epithelium and replicate in enterocytes, both inside Salmonella-specific vacuoles and free in the cytosol (cytosolic hyper-replication). These different phenotypes of intracellular replication drive to different pathways of pathogenesis, i.e., cytosolic hyper-replication induces inflammatory cell death and extrusion into the gut lumen, while vacuolar replication leads to trans-epithelium penetration and systemic spread. Significant effort was made to create microscopy tools to study the behavior of Salmonella inside invaded cells, such as the pCHAR-Duo fluorescence reporter plasmid that allows discrimination between vacuolar and cytosolic bacteria by differential expression of mCherry and GFP. However, intracellular phenotypes are often manually scored, a time-consuming procedure that limits analysis to a small number of samples and cells. To overcome these limitations, two complementary and automated image analyses were developed using ImageJ, a freely available image analysis software. In the high-throughput protocol, epithelial cells were infected with Salmonella carrying pCHAR-Duo using 96-well plates. Imaging was performed using an automated fluorescence microscope. Then, two image analysis methods were applied to measure the intracellular behavior of Salmonella at different detail levels. The first method measures the overall intracellular bacterial load and the extent of cytosolic hyper-replication. It is fast and allows the scoring of a high number of cells and samples, making it suitable for high-throughput assays such as screening experiments. The second method performs single-cell analysis to determine the percentage of infected cells, the mean vacuolar load of Salmonella, and the cytosolic hyper-replication rate giving greater details about Salmonella behavior inside epithelial cells. The protocols can be performed by specifically designed ImageJ scripts to automatically run batch analyses of the major steps of Salmonella-enterocyte interaction. more...
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- 2022
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29. Competition for dominance within replicating quasispecies during prolonged SARS-CoV-2 infection in an immunocompromised host.
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Caccuri F, Messali S, Bortolotti D, Di Silvestre D, De Palma A, Cattaneo C, Bertelli A, Zani A, Milanesi M, Giovanetti M, Campisi G, Gentili V, Bugatti A, Filippini F, Scaltriti E, Pongolini S, Tucci A, Fiorentini S, d'Ursi P, Ciccozzi M, Mauri P, Rizzo R, and Caruso A more...
- Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) emerge for their capability to better adapt to the human host aimed and enhance human-to-human transmission. Mutations in spike largely contributed to adaptation. Viral persistence is a prerequisite for intra-host virus evolution, and this likely occurred in immunocompromised patients who allow intra-host long-term viral replication. The underlying mechanism leading to the emergence of variants during viral persistence in the immunocompromised host is still unknown. Here, we show the existence of an ensemble of minor mutants in the early biological samples obtained from an immunocompromised patient and their dynamic interplay with the master mutant during a persistent and productive long-term infection. In particular, after 222 days of active viral replication, the original master mutant, named MB61
0 , was replaced by a minor quasispecies (MB61222 ) expressing two critical mutations in spike, namely Q493K and N501T. Isolation of the two viruses allowed us to show that MB61222 entry into target cells occurred mainly by the fusion at the plasma membrane (PM), whereas endocytosis characterized the entry mechanism used by MB610 . Interestingly, coinfection of two human cell lines of different origin with the SARS-CoV-2 isolates highlighted the early and dramatic predominance of MB61222 over MB610 replication. This finding may be explained by a faster replicative activity of MB61222 as compared to MB610 as well as by the capability of MB61222 to induce peculiar viral RNA-sensing mechanisms leading to an increased production of interferons (IFNs) and, in particular, of IFN-induced transmembrane protein 1 (IFITM1) and IFITM2. Indeed, it has been recently shown that IFITM2 is able to restrict SARS-CoV-2 entry occurring by endocytosis. In this regard, MB61222 may escape the antiviral activity of IFITMs by using the PM fusion pathway for entry into the target cell, whereas MB610 cannot escape this host antiviral response during MB61222 coinfection, since it has endocytosis as the main pathway of entry. Altogether, our data support the evidence of quasispecies fighting for host dominance by taking benefit from the cell machinery to restrict the productive infection of competitors in the viral ensemble. This finding may explain, at least in part, the extraordinary rapid worldwide turnover of VOCs that use the PM fusion pathway to enter into target cells over the original pandemic strain., (© The Author(s) 2022. Published by Oxford University Press.) more...- Published
- 2022
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30. Versatile Supramolecular Complex for Targeted Antimicrobial Photodynamic Inactivation.
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Mussini A, Uriati E, Hally C, Nonell S, Bianchini P, Diaspro A, Pongolini S, Delcanale P, Abbruzzetti S, and Viappiani C
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- Anti-Bacterial Agents pharmacology, Eosine Yellowish-(YS), Humans, Immunoglobulin G, Photosensitizing Agents chemistry, Photosensitizing Agents pharmacology, Staphylococcus aureus physiology, Streptavidin, Anti-Infective Agents chemistry, Photochemotherapy methods
- Abstract
We report the development of a supramolecular structure endowed with photosensitizing properties and targeting capability for antimicrobial photodynamic inactivation. Our synthetic strategy uses the tetrameric bacterial protein streptavidin, labeled with the photosensitizer eosin, as the main building block. Biotinylated immunoglobulin G (IgG) from human serum, known to associate with Staphylococcus aureus protein A, was bound to the complex streptavidin-eosin. Fluorescence correlation spectroscopy and fluorescence microscopy demonstrate binding of the complex to S. aureus . Efficient photoinactivation is observed for S. aureus suspensions treated with IgG-streptavidin-eosin at concentrations higher than 0.5 μM and exposed to green light. The proposed strategy offers a flexible platform for targeting a variety of molecules and microbial species. more...
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- 2022
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31. Identification of a New Serovar of Salmonella enterica in Mediterranean Buffalo Calves ( Bubalus bubalis ).
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D'Angelo L, Vecchio D, Cozza D, La Tela I, Carullo MR, Menozzi I, Scaltriti E, Pongolini S, Galiero G, and De Carlo E
- Abstract
This case report describes for the first-time cases of severe gastroenteritis in water buffalo calves due to a new serovar of Salmonella enterica . The study was carried out on fecal matrix collected from live water buffalo calves that showed profuse diarrhea, severe dehydration and fever, exhibiting a systemic course. Culture and molecular investigations identified the pathogens isolated from intestinal contents as two Salmonella serovars, Salmonella enterica enterica O:35 and a new serovar of Salmonella enterica . The isolates showed multi-drug resistance. Timely diagnosis associated with a targeted antimicrobial treatment were found to be sufficient for the survival and recovery of the infected animals. Herd vaccines prepared from isolated pathogens were used to prevent further deaths of the calves. more...
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- 2022
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32. Classification of Salmonella enterica of the (Para-)Typhoid Fever Group by Fourier-Transform Infrared (FTIR) Spectroscopy.
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Cordovana M, Mauder N, Kostrzewa M, Wille A, Rojak S, Hagen RM, Ambretti S, Pongolini S, Soliani L, Justesen US, Holt HM, Join-Lambert O, Hello SL, Auzou M, Veloo AC, May J, Frickmann H, and Dekker D
- Abstract
Typhoidal and para-typhoidal Salmonella are major causes of bacteraemia in resource-limited countries. Diagnostic alternatives to laborious and resource-demanding serotyping are essential. Fourier transform infrared spectroscopy (FTIRS) is a rapidly developing and simple bacterial typing technology. In this study, we assessed the discriminatory power of the FTIRS-based IR Biotyper (Bruker Daltonik GmbH, Bremen, Germany), for the rapid and reliable identification of biochemically confirmed typhoid and paratyphoid fever-associated Salmonella isolates. In total, 359 isolates, comprising 30 S . Typhi, 23 S . Paratyphi A, 23 S . Paratyphi B, and 7 S . Paratyphi C, respectively and other phylogenetically closely related Salmonella serovars belonging to the serogroups O:2, O:4, O:7 and O:9 were tested. The strains were derived from clinical, environmental and food samples collected at different European sites. Applying artificial neural networks, specific automated classifiers were built to discriminate typhoidal serovars from non-typhoidal serovars within each of the four serogroups. The accuracy of the classifiers was 99.9%, 87.0%, 99.5% and 99.0% for Salmonella Typhi, Salmonella Paratyphi A, B and Salmonella Paratyphi C, respectively. The IR Biotyper is a promising tool for fast and reliable detection of typhoidal Salmonella . Hence, IR biotyping may serve as a suitable alternative to conventional approaches for surveillance and diagnostic purposes. more...
- Published
- 2021
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33. Economic evaluation of whole genome sequencing for pathogen identification and surveillance - results of case studies in Europe and the Americas 2016 to 2019.
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Alleweldt F, Kara Ş, Best K, Aarestrup FM, Beer M, Bestebroer TM, Campos J, Casadei G, Chinen I, Van Domselaar G, Dominguez C, Everett HE, Fouchier RA, Grant K, Green J, Höper D, Johnston J, Koopmans MP, Oude Munnink BB, Myers R, Nadon C, Patel A, Pohlmann A, Pongolini S, Reimer A, Thiessen S, and Wylezich C more...
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- Americas, Animals, Cost-Benefit Analysis, Europe epidemiology, Genome, Bacterial, Humans, Whole Genome Sequencing, Salmonella Food Poisoning
- Abstract
BackgroundWhole genome sequencing (WGS) is increasingly used for pathogen identification and surveillance.AimWe evaluated costs and benefits of routine WGS through case studies at eight reference laboratories in Europe and the Americas which conduct pathogen surveillance for avian influenza (two laboratories), human influenza (one laboratory) and food-borne pathogens (five laboratories).MethodsThe evaluation focused on the institutional perspective, i.e. the 'investment case' for implementing WGS compared with conventional methods, based on costs and benefits during a defined reference period, mostly covering at least part of 2017. A break-even analysis estimated the number of cases of illness (for the example of Salmonella surveillance) that would need to be avoided through WGS in order to 'break even' on costs.ResultsOn a per-sample basis, WGS was between 1.2 and 4.3 times more expensive than routine conventional methods. However, WGS brought major benefits for pathogen identification and surveillance, substantially changing laboratory workflows, analytical processes and outbreaks detection and control. Between 0.2% and 1.1% (on average 0.7%) of reported salmonellosis cases would need to be prevented to break even with respect to the additional costs of WGS.ConclusionsEven at cost levels documented here, WGS provides a level of additional information that more than balances the additional costs if used effectively. The substantial cost differences for WGS between reference laboratories were due to economies of scale, degree of automation, sequencing technology used and institutional discounts for equipment and consumables, as well as the extent to which sequencers are used at full capacity. more...
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- 2021
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34. Genomic Characterization of VIM and MCR Co-Producers: The First Two Clinical Cases, in Italy.
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Marchetti VM, Bitar I, Sarti M, Fogato E, Scaltriti E, Bracchi C, Hrabak J, Pongolini S, and Migliavacca R
- Abstract
Background: the co-production of carbapenemases and mcr -genes represents a worrisome event in the treatment of Enterobacteriaceae infections. The aim of the study was to characterize the genomic features of two clinical Enterobacter cloacae complex (ECC) isolates, co-producing VIM and MCR enzymes, in Italy., Methods: species identification and antibiotic susceptibility profiling were performed using MALDI-TOF and broth microdilution methods, respectively. Transferability of the bla
VIM- and mcr - type genes was verified through conjugation experiment. Extracted DNA was sequenced using long reads sequencing technology on the Sequel I platform (PacBio)., Results: the first isolate showed clinical resistance against ertapenem yet was colistin susceptible (EUCAST 2020 breakpoints). The mcr-9.2 gene was harbored on a conjugative IncHI2 plasmid, while the blaVIM-1 determinant was harbored on a conjugative IncN plasmid. The second isolate, resistant to both carbapenems and colistin, harbored: mcr-9 gene and its two component regulatory genes for increased expression on the chromosome, mcr-4.3 on non-conjugative (yet co-transferable) ColE plasmid, and blaVIM-1 on a non-conjugative IncA plasmid., Conclusions: to our knowledge, this is the first report of co-production of VIM and MCR in ECC isolates in Italy. more...- Published
- 2021
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35. Mutation of hilD in a Salmonella Derby lineage linked to swine adaptation and reduced risk to human health.
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Tambassi M, Berni M, Bracchi C, Scaltriti E, Morganti M, Bolzoni L, Tanner JR, Thilliez G, Kingsley RA, Pongolini S, and Casadei G
- Subjects
- Animals, Bacterial Proteins metabolism, Gene Expression Regulation, Bacterial genetics, Genomic Islands genetics, Humans, Mutation genetics, Phylogeny, Salmonella Infections, Animal genetics, Salmonella enterica metabolism, Salmonella enterica pathogenicity, Serogroup, Swine, Transcription Factors metabolism, Virulence Factors genetics, Bacterial Proteins genetics, Salmonella Infections genetics, Salmonella enterica genetics, Transcription Factors genetics
- Abstract
Salmonella enterica variants exhibit diverse host adaptation, outcome of infection, and associated risk to food safety. Analysis of the distribution of Salmonella enterica serovar Derby (S. Derby) subtypes in human and swine identified isolates with a distinct PFGE profile that were significantly under-represented in human infections, consistent with further host adaptation to swine. Here we show that isolates with this PFGE profile form a distinct phylogenetic sub-clade within S. Derby and exhibit a profound reduction in invasion of human epithelial cells, and a relatively small reduction in swine epithelial cells. A single missense mutation in hilD, that encodes the master-regulator of the Salmonella Pathogenicity Island 1 (SPI-1), was present in the adapted lineage. The missense mutation resulted in a loss of function of HilD that accounted for reduced invasion in human epithelial cells. The relatively small impact of the mutation on interaction with swine cells was consistent with an alternative mechanism of invasion in this pathogen-host combination. more...
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- 2020
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36. Paratuberculosis in Captive Scimitar-Horned Oryxes ( Oryx dammah ).
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Pigoli C, Garbarino C, Ricchi M, Bonacina E, Gibelli L, Grieco V, Scaltriti E, Roccabianca P, Sironi G, Russo S, Pongolini S, and Arrigoni N
- Abstract
Paratuberculosis, a chronic disease caused by Mycobacterium avium subsp. paratuberculosis (MAP), in ten scimitar-horned oryxes (SHOs) hosted in an Italian zoological park and originating from a Slovakian flock, was documented by pathology, molecular, cultural, and serological testing. The infection origin in this threatened species was also investigated by genomic analyses. Following the death of six of the 10 SHOs, serial investigations of dead and alive animals were performed. Necropsy, carried out on five out of six animals, identified intestinal thickening and mesenteric lymphadenomegaly in one of the animals. Histopathology (5/6) revealed lepromatous (2/5) and tuberculoid (2/5) intestinal forms or lack of lesions (1/5). Ziehl-Neelsen and immunohistochemistry stains identified two multibacillary, two paucibacillary forms, and one negative case. MAP was identified by quantitative PCR (qPCR) in tissue samples in five out of five SHOs and was microbiologically isolated from two of the three animals whose fresh tissue samples were available. Fecal samples were collected in four of the six dead animals: all four resulted positive to qPCR and in MAP was isolated in three. ELISA identified MAP-specific antibodies in three of the five dead animals whose serum was available. qPCR identified MAP in the freshly deposited feces of two out of the four alive animals. From the feces of these two animals, MAP was microbiologically isolated in one case. All isolates were classified as MAP type C and profiled as INMV2 and MVS27 by molecular analysis. Genomic analysis of a field isolate revealed clusterization with a European clade but was more similar to Italian than East European isolates. Our findings underline that paratuberculosis should always be considered in zoological parks in which endangered species are hosted. Infection can be subclinical, and multiple combined testing techniques may be necessary. more...
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- 2020
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37. Population Structure of Listeria monocytogenes in Emilia-Romagna (Italy) and Implications on Whole Genome Sequencing Surveillance of Listeriosis.
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Scaltriti E, Bolzoni L, Vocale C, Morganti M, Menozzi I, Re MC, and Pongolini S
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- Food Microbiology, Genome, Bacterial genetics, Humans, Italy epidemiology, Multilocus Sequence Typing, Whole Genome Sequencing, Listeria monocytogenes genetics, Listeriosis epidemiology
- Abstract
The population structure of human isolates of Listeria monocytogenes in Emilia-Romagna, Italy, from 2012 to 2018 was investigated with the aim of evaluating the presence of genomic clusters indicative of possible outbreaks, the proportion of cluster-associated vs. sporadic isolates and different methods and metrics of genomic analysis for use in routine surveillance. In the 2012-2018 period the notification rate of confirmed invasive cases in Emilia-Romagna was 0.91 per 100,000 population per year, more than twice the average rate of EU countries. Out of the total 283 cases, 268 (about 95%) isolates were typed through whole genome sequencing (WGS) for cluster detection with methods based on core-genome multi-locus sequence typing and single nucleotide polymorphisms. Between 66 and 72% of listeriosis cases belonged to genomic clusters which included up to 27 cases and lasted up to 5 years. This proportion of cluster-associated cases is higher than previously estimated in other European studies. Rarefaction analysis, performed by reducing both the number of consecutive years of surveillance considered and the proportion of isolates included in the analysis, suggested that the observed high proportion of cluster-associated cases can be ascribed to the long surveillance duration (7 years) and the high notification and typing rates of this study. Our findings show that a long temporal perspective and high surveillance intensity, intended as both exhaustiveness of the system to report cases and high WGS-typing rate, are critical for sensitive detection of possible outbreaks within a WGS-based surveillance of listeriosis. Furthermore, the power and complexity of WGS interpretation emerged from the integration of genomic and epidemiological information in the investigation of few past outbreaks within the study, indicating that the use of multiple approaches, including the analysis of the accessory genome, is needed to accurately elucidate the population dynamics of Listeria monocytogenes ., (Copyright © 2020 Scaltriti, Bolzoni, Vocale, Morganti, Menozzi, Re and Pongolini.) more...
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- 2020
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38. Draft Genome Sequence of Listeria monocytogenes Serovar 1/2a Strain IZSAM_Lm_14-16064, Isolated from an Italian Cooked Ham in 2014.
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Di Lollo V, Orsini M, Acciari V, Cammà C, Centorame P, Centorotola G, Curini V, Di Pasquale A, Rinaldi A, Pongolini S, Torresi M, and Pomilio F
- Abstract
In this report, the draft genome sequence of Listeria monocytogenes serovar 1/2a strain IZSAM_Lm_14-16064, isolated in Italy from a cooked ham, is announced. The genome is similar to that of a clinical strain isolated in 2014., (Copyright © 2020 Di Lollo et al.) more...
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- 2020
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39. Complete Genome Sequence of Chlamydia avium PV 4360/2, Isolated from a Feral Pigeon in Italy.
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Floriano AM, Rigamonti S, Comandatore F, Scaltriti E, Longbottom D, Livingstone M, Laroucau K, Gaffuri A, Pongolini S, Magnino S, and Vicari N
- Abstract
We report here the whole-genome sequence of a Chlamydia avium isolate recovered from a feral pigeon in 1999 in Italy. Only one complete genome of a C. avium strain has been published so far. Future comparative analyses could provide valuable insights on the genomic evolution of the pathogen., (Copyright © 2020 Floriano et al.) more...
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- 2020
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40. Gene Composition as a Potential Barrier to Large Recombinations in the Bacterial Pathogen Klebsiella pneumoniae.
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Comandatore F, Sassera D, Bayliss SC, Scaltriti E, Gaiarsa S, Cao X, Gales AC, Saito R, Pongolini S, Brisse S, Feil EJ, and Bandi C
- Subjects
- Clone Cells microbiology, Genome, Bacterial, Humans, Klebsiella Infections epidemiology, Klebsiella Infections microbiology, Klebsiella pneumoniae genetics, Recombination, Genetic
- Abstract
Klebsiella pneumoniae (Kp) is one of the most important nosocomial pathogens worldwide, able to cause multiorgan infections and hospital outbreaks. One of the most widely disseminated lineage of Kp is the clonal group 258 (CG258), which includes the highly resistant "high-risk" sequence types ST258 and ST11. Genomic investigations revealed that very large recombination events have occurred during the emergence of Kp lineages. A striking example is provided by ST258, which has undergone a recombination event that replaced over 1 Mb of the genome with DNA from an unrelated Kp donor. Although several examples of this phenomenon have been documented in Kp and other bacterial species, the significance of these very large recombination events for the emergence of either hypervirulent or resistant clones remains unclear. Here, we present an analysis of 834 Kp genomes that provides data on the frequency of these very large recombination events (defined as those involving >100 kb), their distribution within the genome, and the dynamics of gene flow within the Kp population. We note that very large recombination events occur frequently, and in multiple lineages, and that the majority of recombinational exchanges are clustered within two overlapping genomic regions, which have been involved by recombination events with different frequencies. Our results also indicate that certain lineages are more likely to act as donors to CG258. Furthermore, comparison of gene content in CG258 and non-CG258 strains agrees with this pattern, suggesting that the success of a large recombination depends on gene composition in the exchanged genomic portion., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.) more...
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- 2019
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41. Can Insertion Sequences Proliferation Influence Genomic Plasticity? Comparative Analysis of Acinetobacter baumannii Sequence Type 78, a Persistent Clone in Italian Hospitals.
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Gaiarsa S, Bitar I, Comandatore F, Corbella M, Piazza A, Scaltriti E, Villa L, Postiglione U, Marone P, Nucleo E, Pongolini S, Migliavacca R, and Sassera D
- Abstract
Acinetobacter baumannii is a known opportunistic pathogen, dangerous for public health mostly due to its ability to rapidly acquire antibiotic-resistance traits. Its genome was described as characterized by remarkable plasticity, with a high frequency of homologous recombinations and proliferation of Insertion Sequences (IS). The SMAL pulsotype is an A. baumannii strain currently isolated only in Italy, characterized by a low incidence and a high persistence over the years. In this present work, we have conducted a comparative genomic analysis on this clone. The genome of 15 SMAL isolates was obtained and characterized in comparison with 24 other assemblies of evolutionary related isolates. The phylogeny highlighted the presence of a monophyletic clade (named ST78A), which includes the SMAL isolates. ST78A isolates have a low rate of homologous recombination and low gene content variability when compared to two related clades (ST78B and ST49) and to the most common A. baumannii variants worldwide (International Clones I and II). Remarkably, genomes in the ST78A clade present a high number of IS, including classes mostly absent in the other related genomes. Among these IS, one copy of IS66 was found to interrupt the gene comEC/rec2 , involved in the acquisition of exogenous DNA. The genomic characterization of SMAL isolates shed light on the surprisingly low genomic plasticity and the high IS proliferation present in this strain. The interruption of the gene comEC / rec2 by an IS in the SMAL genomes brought us to formulate an evolutionary hypothesis according to which the proliferation of IS is slowing the acquisition of exogenous DNA, thus limiting genome plasticity. Such genomic architecture could explain the epidemiological behavior of high persistence and low incidence of the clone and provides an interesting framework to compare ST78 with the highly epidemic International Clones, characterized by high genomic plasticity., (Copyright © 2019 Gaiarsa, Bitar, Comandatore, Corbella, Piazza, Scaltriti, Villa, Postiglione, Marone, Nucleo, Pongolini, Migliavacca and Sassera.) more...
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- 2019
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42. Limited Exchange of Salmonella Among Domestic Pigs and Wild Boars in Italy.
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Bonardi S, Bolzoni L, Zanoni RG, Morganti M, Corradi M, Gilioli S, and Pongolini S
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- Age Factors, Animals, Drug Resistance, Bacterial, Feces microbiology, Female, Italy epidemiology, Lymph Nodes microbiology, Male, Microbial Sensitivity Tests, Salmonella classification, Swine, Swine Diseases microbiology, Temperature, Salmonella isolation & purification, Salmonella Infections, Animal epidemiology, Sus scrofa microbiology, Swine Diseases epidemiology
- Abstract
The study assessed Salmonella carriage in wild boars (Sus scrofa) and compared their isolates with those recovered from the domestic swine population of the same area of northern Italy (Emilia-Romagna), characterized by intensive pig farming and rather high density of wild boars. A total of 189 wild boars hunted during twelve months (2017-2018) were tested for Salmonella in mesenteric lymph nodes (MLN) and faecal samples. Antimicrobial resistance of recovered strains was tested against 14 antimicrobials. Salmonella was detected in 33/189 wild boars (17.5%), specifically from 30/189 MLN (15.9%) and 6/189 faecal samples (3.2%). Three animals were positive in both samples. Thirteen Salmonella serovars were identified, i.e. Typhimurium (the most common), Bovismorbificans, Coeln, Derby, Enteritidis, Gaminara, Hessarek, Houtenae IV, Kottbus, Napoli, Stanleyville, Thompson and Veneziana. Salmonella carriage was higher in warm than in cold months (P = 0.0013). Pregnancy status was never associated with Salmonella carriage, with significant difference in the recovery of the pathogen between non-pregnant and pregnant females (P = 0.003). Only one resistance pattern to streptomycin and tetracycline was found in 15 isolates (41.7%) belonging to Typhimurium (14/14; 100%) and Kottbus (1/3; 33.3%) serovars. Overlap with isolates from farmed pigs was limited at serotype level (Typhimurium, Derby, Enteritis, Bovismorbificans, Kottbus) and absent at PFGE level, and also antimicrobial resistance patterns were substantially different. This evidence indicates a substantial segregation of the two animal populations with regard to infectious contacts, possibly suggesting that biosecurity measures in place at industrial farm level limit the exchange of Salmonella. more...
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- 2019
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43. A novel IncA plasmid carrying blaVIM-1 in a Kluyvera cryocrescens strain.
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Gaibani P, Ambretti S, Scaltriti E, Cordovana M, Berlingeri A, Pongolini S, Landini MP, and Re MC
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- Base Sequence, Enterobacteriaceae Infections microbiology, Female, Genome, Bacterial, Humans, Italy, Kluyvera enzymology, Plasmids isolation & purification, Rectum microbiology, Whole Genome Sequencing, Bacterial Proteins genetics, Carbapenem-Resistant Enterobacteriaceae isolation & purification, Kluyvera drug effects, Kluyvera genetics, Plasmids genetics, beta-Lactamases genetics
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- 2018
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44. High-resolution diffusion pattern of human infections by Salmonella enterica serovar Napoli in Northern Italy explained through phylogeography.
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Gori M, Ebranati E, Scaltriti E, Huedo P, Ciceri G, Tanzi E, Pontello M, Zehender G, Pongolini S, and Bolzoni L
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- Disease Outbreaks, Humans, Italy epidemiology, Phylogeny, Salmonella Food Poisoning epidemiology, Salmonella Food Poisoning microbiology, Salmonella Infections epidemiology, Salmonella Infections microbiology, Salmonella enterica pathogenicity, Serogroup, Phylogeography, Salmonella Food Poisoning genetics, Salmonella Infections genetics, Salmonella enterica genetics
- Abstract
Salmonella enterica serovar Napoli (serovar Napoli) is an emerging cause of human salmonellosis in Northern Italy. No specific reservoirs of serovar Napoli have been identified in Italy, so far. However, the environment, especially surface waters, has been hypothesized as an important source of infection based on the observation that genotypically different clusters of serovar Napoli are detected in different geographical macro-areas. To further support the hypothesis of a spatially-restricted pattern of serovar Napoli diffusion, a spatial segregation of serovar Napoli lineages should be observed also at smaller geographical scale. However, classical genotyping techniques used for Salmonella, such as pulsed-field gel electrophoresis (PFGE), did not possess enough discriminatory power to highlight spatial clustering of serovar Napoli within the macro-areas. To this purpose, we performed phylogeographical analyses based on genome-wide single nucleotide polymorphisms to test whether spatio-temporal evolution patterns of serovar Napoli in Northern Italy could be recognized with high geographical resolution, i.e. at local level. Specifically, we analyzed the local spread of the main PFGE clonal group, responsible for more than 60% of human infections in the study area, that did not show any geographical differentiation by PFGE within Northern Italy, i.e. the macro-area considered in the study. Both discrete and continuous phylogeography highlighted the existence of two main geographically-restricted clades: a Southern clade corresponding to the Po Valley and a Northern clade corresponding to the Pre-Alps area. Furthermore, the phylogeographical analyses suggested that the most probable site of origin of the clone was in an area of the Po Valley at the confluence of the Po and Ticino rivers, one of the most important Italian wetlands. These findings provide further support to the hypothesis that environmental transmission may play an important role in the ecology of serovar Napoli., Competing Interests: The authors have declared that no competing interests exist. more...
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- 2018
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45. Salmonella Detection and Counting on Pig Carcasses and Cutting Lines in Italian Slaughterhouses.
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Bonardi S, Bolzoni L, Brindani F, Scaltriti E, Cavallini P, Giuseppe C, and Pongolini S
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- Abattoirs, Animals, Food Microbiology, Food-Processing Industry, Italy epidemiology, Prevalence, Salmonella isolation & purification, Serogroup, Food Contamination, Red Meat microbiology, Salmonella immunology, Swine microbiology
- Abstract
During 2014-2015, 300 pig carcasses before chilling and 85 food contact surfaces (FCSs) at cutting lines were tested for Salmonella in three slaughterhouses (namely A, B, and C) of northern Italy. In slaughterhouses A and B, four carcass sites of 100 cm
2 each (from both the exterior and interior side) were swabbed with a single sponge. In abattoir C, four 100 cm2 sites of the exterior and the interior sides were swabbed with two independent sponges. The population average prevalence of Salmonella-positive carcasses (which takes into account the structure of the study design, with multiple samples collected in a single day) in slaughterhouses A and B was 12.3%, while in slaughterhouse C it was 11.2%. Presence of Salmonella on exterior and interior sides of carcasses showed a low level of concordance (only 3/12 of the contaminated carcasses were positive on both sides). No significant difference was found for FCSs contamination in the three slaughterhouses, with a population average prevalence of Salmonella-positive FCSs of 19.9%. In addition, we found that the clustering due to the day of sampling account for more than 36% and 60% of the overall prevalence variation on carcasses and FCSs, respectively. Eight serovars were identified, with Salmonella Derby as the most common type. The counting of Salmonella on carcasses showed large variability. It was low (<0.0075 most probable number [MPN]/cm2 ) in 46.6% of the carcasses and as high as 2.7 MPN/cm2 in 4.7%. Specifically, we found that counts on carcasses fit with "heavy tailed" distributions (lognormal and Weibull with a small shape parameter), suggesting not negligible probability of episodes of high Salmonella contamination. The mean values of contamination obtained with the two distributions ranged from 0.235 to 0.435 MPN/cm2 . more...- Published
- 2018
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46. In vivo evolution of resistant subpopulations of KPC-producing Klebsiella pneumoniae during ceftazidime/avibactam treatment.
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Gaibani P, Campoli C, Lewis RE, Volpe SL, Scaltriti E, Giannella M, Pongolini S, Berlingeri A, Cristini F, Bartoletti M, Tedeschi S, and Ambretti S
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- Anti-Bacterial Agents therapeutic use, Bacterial Proteins genetics, Carbapenem-Resistant Enterobacteriaceae isolation & purification, Drug Combinations, Humans, Klebsiella Infections blood, Klebsiella Infections microbiology, Klebsiella pneumoniae enzymology, Microbial Sensitivity Tests, Mutation, Phylogeny, Porins genetics, Whole Genome Sequencing, beta-Lactamases genetics, Azabicyclo Compounds therapeutic use, Carbapenem-Resistant Enterobacteriaceae genetics, Ceftazidime therapeutic use, Drug Resistance, Multiple, Bacterial genetics, Evolution, Molecular, Klebsiella pneumoniae drug effects, Klebsiella pneumoniae genetics
- Abstract
Objectives: KPC-producing Klebsiella pneumoniae (KPC-Kp) represent a serious problem worldwide. Herein, we describe the evolution of ceftazidime/avibactam resistance by sequencing longitudinal clinical isolates from a patient with KPC-Kp bloodstream infection undergoing ceftazidime/avibactam treatment., Methods: WGS was performed on one ceftazidime/avibactam-susceptible KPC-Kp (BOT-CA-S) and two phenotypically different ceftazidime/avibactam-resistant KPC-Kp with low (BOT-CA-R) and high (BOT-EMO) carbapenem MICs. The population diversity was assessed by the frequency of allele mutations and population analysis profiles (PAPs)., Results: Phylogenetic analysis demonstrated clonal relatedness of the KPC-Kp isolates, all belonging to the clone ST1519. The D179Y mutation in blaKPC-3 was detected in both of the ceftazidime/avibactam-resistant KPC-Kp, whereas it was absent in the ceftazidime/avibactam-susceptible isolate. The mutation emerged independently in the two ceftazidime/avibactam-resistant isolates and was associated with a significant reduction in carbapenem MICs in BOT-CA-R, but not in BOT-EMO. WGS analysis revealed that the frequency of the D179Y mutation was 96.32% and 51.05% in BOT-CA-R and BOT-EMO, respectively. PAP results demonstrated that carbapenem resistance in BOT-EMO was due to the coexistence of mixed subpopulations harbouring WT and mutated blaKPC-3. A bacterial subpopulation with high ceftazidime/avibactam resistance for BOT-EMO KPC-Kp showed low carbapenem MICs, whereas a subpopulation with high meropenem resistance had a low MIC of ceftazidime/avibactam., Conclusions: Our analysis indicates that mixed subpopulations of ceftazidime/avibactam-resistant KPC-Kp emerge after ceftazidime/avibactam treatment. The evolution of different subpopulations that are highly resistant to ceftazidime/avibactam likely contributes to treatment failure, thereby highlighting the need for combination treatment strategies to limit selection of ceftazidime/avibactam-resistant KPC-Kp subpopulations. more...
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- 2018
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47. Rise and fall of outbreak-specific clone inside endemic pulsotype of Salmonella 4,[5],12:i:-; insights from high-resolution molecular surveillance in Emilia-Romagna, Italy, 2012 to 2015.
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Morganti M, Bolzoni L, Scaltriti E, Casadei G, Carra E, Rossi L, Gherardi P, Faccini F, Arrigoni N, Sacchi AR, Delledonne M, and Pongolini S
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- Bacterial Typing Techniques methods, Electrophoresis, Gel, Pulsed-Field, Humans, Italy epidemiology, Molecular Epidemiology, Molecular Typing methods, Polymorphism, Single Nucleotide, Retrospective Studies, Salmonella classification, Salmonella Infections diagnosis, Whole Genome Sequencing, DNA, Bacterial genetics, Disease Outbreaks, Endemic Diseases, Minisatellite Repeats genetics, Salmonella genetics, Salmonella isolation & purification, Salmonella Infections epidemiology, Salmonella Infections microbiology
- Abstract
Background and aimEpidemiology of human non-typhoid salmonellosis is characterised by recurrent emergence of new clones of the pathogen over time. Some clonal lines of Salmonella have shaped epidemiology of the disease at global level, as happened for serotype Enteritidis or, more recently, for Salmonella 4,[5],12:i:-, a monophasic variant of serotype Typhimurium. The same clonal behaviour is recognisable at sub-serotype level where single outbreaks or more generalised epidemics are attributable to defined clones. The aim of this study was to understand the dynamics of a clone of Salmonella 4,[5],12:i:- over a 3-year period (2012-15) in a province of Northern Italy where the clone caused a large outbreak in 2013. Furthermore, the role of candidate outbreak sources was investigated and the accuracy of multilocus variable-number tandem repeat analysis (MLVA) was evaluated. Methods: we retrospectively investigated the outbreak through whole genome sequencing (WGS) and further monitored the outbreak clone for 2 years after its conclusion. Results: The study showed the transient nature of the clone in the population, possibly as a consequence of its occasional expansion in a food-processing facility. We demonstrated that important weaknesses characterise conventional typing methods applied to clonal pathogens such as Salmonella 4,[5],12:i:-, namely lack of accuracy for MLVA and inadequate resolution power for PFGE to be reliably used for clone tracking. Conclusions : The study provided evidence for the remarkable prevention potential of whole genome sequencing used as a routine tool in systems that integrate human, food and animal surveillance. more...
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- 2018
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48. Isolation of three novel reassortant phleboviruses, Ponticelli I, II, III, and of Toscana virus from field-collected sand flies in Italy.
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Calzolari M, Chiapponi C, Bellini R, Bonilauri P, Lelli D, Moreno A, Barbieri I, Pongolini S, Lavazza A, and Dottori M
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- Animals, Cluster Analysis, Genome, Viral, Genotype, Italy, Phlebovirus genetics, Phylogeny, Reassortant Viruses genetics, Sequence Analysis, DNA, Sequence Homology, Genetic Variation, Phlebovirus classification, Phlebovirus isolation & purification, Psychodidae virology, Reassortant Viruses classification, Reassortant Viruses isolation & purification
- Abstract
Background: Different phleboviruses are important pathogens for humans; most of these viruses are transmitted by sand flies. An increasing number of new phleboviruses have been reported over the past decade, especially in Mediterranean countries, mainly via their detection in sand flies., Results: At least five different phleboviruses co-circulated in sand flies that were collected in three sites in Emilia-Romagna (Italy) in the summer of 2013. The well-known Toscana virus (TOSV) was isolated; three new, closely related phleboviruses differing in their M segments and tentatively named Ponticelli I, Ponticelli II and Ponticelli III virus, respectively, were isolated; a fifth putative phlebovirus, related to the sand fly fever Naples phlebovirus species, was also detected. The co-circulation, in a restricted area, of three viruses characterized by different M segments, likely resulted from reassortment events. According to the phylogenetic analysis of complete genome sequences, the TOSV belongs to clade A, together with other Italian isolates, while the Ponticelli viruses fall within the Salehabad phlebovirus species., Conclusions: Results highlight an unexpected diversity of phleboviruses that co-circulate in the same area, suggesting that interactions likely occur amongst them, that can present challenges for their correct identification. The co-circulation of different phleboviruses appears to be common, and the bionomics of sand fly populations seem to play a relevant role. Such a complex situation emphasizes the need for detailed investigations of the biology of these viruses to better characterize their pathogenic potential for mammals, including humans. more...
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- 2018
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49. Characterization of hazards, welfare promoters and animal-based measures for the welfare assessment of dairy cows: Elicitation of expert opinion.
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Bertocchi L, Fusi F, Angelucci A, Bolzoni L, Pongolini S, Strano RM, Ginestreti J, Riuzzi G, Moroni P, and Lorenzi V
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- Animals, Cattle, Delphi Technique, Female, Italy, Animal Welfare legislation & jurisprudence, Dairying methods, Housing, Animal, Veterinarians psychology
- Abstract
An expert opinion elicitation, based on a modified Delphi technique, was organized to collect the opinion of 16 Italian veterinarians with the aim of conducting a hazard and a welfare promoter characterization for defining and weighing a list of management and housing factors potentially associated with negative or positive welfare outcomes in dairy cows kept in loose housing systems. In addition, the 16 experts judged a set of animal-based measures in order to rate them by appropriateness and by the level of animal pain and suffering due to the welfare consequences they measure. Veterinary experts were asked to score 52 hazards, 47 welfare promoters and 18 animal-based measures. Management and housing hazards, that were determined to be associated with a very high impact on the welfare of dairy cows, were mainly referred to lactating cows (absence of bedding material, presence of inadequate or slippery floor in walking areas, wrong design of the lying area), but also the use of harmful tools for animal handling and the lack of scheduled foot inspection, trimming and foot bathing reached very high impact scores. Management and housing welfare promoters dealing with optimal cow comfort around resting obtained the highest ratings, together with the presence of experienced and trained stockpersons, the implementation of an attentive animal grouping strategy and the control of temperature, humidity and ventilation. Considering animal-based measures, the highest ranking of importance was given to observation of lameness, records of mortality of adult cows and calves, observation of integument alterations and body condition scoring. This study has been the starting point for the development of the first Italian national protocol for the assessment of the welfare of dairy cows farmed in loose housing systems., (Copyright © 2017 Elsevier B.V. All rights reserved.) more...
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- 2018
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50. Detection of mcr-4 positive S almonella enterica serovar Typhimurium in clinical isolates of human origin, Italy, October to November 2016.
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Carretto E, Brovarone F, Nardini P, Russello G, Barbarini D, Pongolini S, Gagliotti C, Carattoli A, and Sarti M
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- Bacterial Proteins genetics, Colistin pharmacology, Gastroenteritis microbiology, Genes, Bacterial, Humans, Italy, Microbial Sensitivity Tests, Salmonella typhimurium drug effects, Sequence Analysis, DNA, Serogroup, Anti-Bacterial Agents pharmacology, Drug Resistance, Bacterial genetics, Feces microbiology, Gastroenteritis diagnosis, Salmonella typhimurium genetics, Salmonella typhimurium isolation & purification
- Abstract
In this study we report the detection of the recently described mcr-4 gene in two human isolates of Salmonella enterica serovar Typhimurium. The strains were isolated from faecal samples of two Italian patients with gastroenteritis, collected in 2016. The identified mcr-4 genes (variant mcr-4.2 ) differed from the mcr-4 gene originally described in a Salmonella strain of swine origin from Italy. Salmonella species could represent a hidden reservoir for mcr genes. more...
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- 2018
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