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2. Wastewater surveillance of SARS-CoV-2 variants in October–November 2022 in Italy: detection of XBB.1, BA.2.75 and rapid spread of the BQ.1 lineage

Author

Palma, Achille, Calabria, Adelaide, Carnevali, Agnese, Nehludoff, Albano, Stenico, Alberta, Izzotti, Alberto, Barca, Alessandra, Tosco, Alessandra, Porta, Amalia, Lombardi, Annalisa, Voli, Antonia, Franzetti, Andrea, Ciccaglione, Angela, Costa, Angela, D’Argenzio, Angelo, Romano, Angelo, Pariani, Anna, Carducci, Annalaura, Grucci, Annalisa, Prast, Anna-Maria, Agodi, Antonella, Cersini, Antonella, Giorgi, Antonella, Bertasi, Barbara, Griglio, Bartolomeo, Ancona, Carla, Maida, Carmelo Massimo, Montanaro, Carmen, Filizzolo, Chiara, Ottaviano, Claudio, Cocuzza, Clementina, Pignata, Cristina, Nasci, Daniele, Cereda, Danilo, Oliva, Desdemona, Giorgi, Doriana Antonella, Malacaria, Edoardo, Grasselli, Elena, Nicosia, Elena, Carraro, Elisabetta, Ammoni, Emanuela, Grange, Eric, Federici, Ermanno, Filippetti, Fabio, Tramuto, Fabio, Guarneri, Flavia, Serio, Flavia, Damasco, Florida, Palumbo, Franca, Apollonio, Francesca, Cutrupi, Francesca, Gucciardi, Francesca, Pennino, Francesca, Russo, Francesca, Triggiano, Francesco, Rigoli, Franco, Pietrella, Gabriele, Trani, Gabriella, Rossolini, Gian Maria, Bulotta, Giorgia, Fusco, Giovanna, La Vecchia, Giovanna, Alborali, Giovanni, Giammanco, Giovanni, Santoro, Giovanni, Pitter, Gisella, Purpari, Giuseppa, Aprea, Giuseppe, Di Vittorio, Giuseppe, Folino, Giuseppe, Lauria, Giuseppe, Federigi, Ileana, Amoruso, Irene, Ferrante, Irene, Tomesani, Irene, De Lellis, Laura, Pellegrinelli, Laura, Demetz, Lea, Gentili, Lisa, Richiardi, Lisa, Zago, Lorella, Masieri, Lorena, Decastelli, Lucia, Bolognini, Luigi, Cossentino, Luigi, Bianchi, Manila, Verani, Marco, Zampini, Marco, Ferrante, Margherita, Cadonna, Maria, Montagna, Maria Teresa, Scicluna, Maria Teresa, Arizzi, Mariaconcetta, Mariuz, Marika, Palermo, Mario, Bellisomi, Marta, Paniccià, Marta, Barchitta, Martina, Ramazzotti, Matteo, Postinghel, Mattia, Viscardi, Maurizio, Ruffier, Mauro, Petricciuolo, Maya, La Bianca, Michele, Colitti, Michele, Monfrinotti, Monica, Fontani, Nadia, Formenti, Nicoletta, Mongelli, Onofrio, De Giglio, Osvalda, Angelini, Paola, Foladori, Paola, Torlontano, Paolo, Calà, Piergiuseppe, Cifarelli, Rosa Anna, Binda, Sandro, Briscolini, Sara, Castiglioni, Sara, Bonetta, Silvia, Magi, Silvia, Scattolini, Silvia, Schiarea, Silvia, De Grazia, Simona, Rosatto, Stefano, Baldovin, Tatjana, Primache, Valeria, Groppi, Vanessa, Acciari, Vicdalia Aniela, Mazzucco, Walter, La Rosa, G., Brandtner, D., Bonanno Ferraro, G., Veneri, C., Mancini, P., Iaconelli, M., Lucentini, L., Del Giudice, C., Orlandi, L., and Suffredini, E.

Published
2023
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3. The rapid spread of SARS-COV-2 Omicron variant in Italy reflected early through wastewater surveillance

Author

Palma, Achille, Stenico, Alberta, Antonelli, Alberto, Izzotti, Alberto, Schiavuzzi, Alessandra, Tosco, Alessandra, Porta, Amalia, Franzetti, Andrea, Turolla, Andrea, Costa, Angela, D’Argenzio, Angelo, Romano, Angelo, Pariani, Anna, Carducci, Annalaura, Prast, Anna-Maria, Agodi, Antonella, Cersini, Antonella, Pizzolante, Antonio, Azzellino, Arianna, Bertasi, Barbara, Griglio, Bartolomeo, Ancona, Carla, Maida, Carmelo Massimo, Montanaro, Carmen, Ottaviano, Claudio, Cocuzza, Clementina, Pignata, Cristina, Nasci, Daniele, Cereda, Danilo, Oliva, Desdemona, Giorgi, Doriana Antonella, Grasselli, Elena, Mengon, Elena, Nicosia, Elena, Carraro, Elisabetta, Ammoni, Emanuela, Ricci, Enrica, Grange, Eric, Federici, Ermanno, Zuccato, Ettore, Filippetti, Fabio, Zuccon, Fabio, Guarneri, Flavia, Damasco, Florida, Palumbo, Franca, Apollonio, Francesca, Borney, Francesca, Ciuti, Francesca, Cutrupi, Francesca, Malpei, Francesca, Pennino, Francesca, Russo, Francesca, Pizzo, Francesco, Triggiano, Francesco, Rigoli, Franco, Trani, Gabriella, Cecchini, Giancarlo, Borlone, Gianluca, Allaria, Giorgia, Bertanza, Giorgio, Fusco, Giovanna, La Vecchia, Giovanna, Alborali, Giovanni, Giammanco, Giovanni, Santoro, Giovanni, Pitter, Gisella, Lauretani, Giulia, Nani, Giulia, Purpari, Giuseppa, Aprea, Giuseppe, Bucciarelli, Giuseppe, Di Vittorio, Giuseppe, Lauria, Giuseppe, Federigi, Ileana, Amoruso, Irene, Ferrante, Irene, De Lellis, Laura, Gentili, Lisa, Zago, Lorella, Decastelli, Lucia, Bolognini, Luigi, Cossentino, Luigi, Bianchi, Manila, Antonelli, Manuela, Guercio, Marco, Verani, Marco, Zampini, Marco, Ferrante, Margherita, Cadonna, Maria, Cerroni, Maria Grazia, Callegari, Maria Luisa, Montagna, Maria Teresa, Scicluna, Maria Teresa, Arizzi, Mariaconcetta, Mariuz, Marika, Losio, Marina Nadia, Palermo, Mario, Paniccià, Marta, Triassi, Maria, Barchitta, Martina, Ramazzotti, Matteo, Postinghel, Mattia, Cravero, Mauro, Ruffier, Mauro, Petricciuolo, Maya, La Bianca, Michele, Colitti, Michele, Monfrinotti, Monica, Fontani, Nadia, Ungaro, Nicola, Formenti, Nicoletta, Mongelli, Onofrio, De Giglio, Osvalda, Angelini, Paola, Foladori, Paola, Torlontano, Paolo, Montenegro, Patrizia, Laura, Pellegrinelli, Calà, Piergiuseppe, Olivares, Renato, Berruti, Renza, Cifarelli, Rosa Anna, Brienza, Rosanna, Binda, Sandro, Briscolini, Sara, Castiglioni, Sara, Muzio, Sara, Manara, Serena, Bonetta, Silvia, Magi, Silvia, Riosa, Silvia, Schiarea, Silvia, De Grazia, Simona, Barigelli, Sofia, Rosatto, Stefano, Baldovin, Tatjana, Capparuccini, Valeria, Primache, Valeria, Groppi, Vanessa, Mazzucco, Walter, La Rosa, G., Iaconelli, M., Veneri, C., Mancini, P., Bonanno Ferraro, G., Brandtner, D., Lucentini, L., Bonadonna, L., Rossi, M., Grigioni, M., and Suffredini, E.

Published
2022
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4. Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater

Author

Lee, Wei Lin, Armas, Federica, Guarneri, Flavia, Gu, Xiaoqiong, Formenti, Nicoletta, Wu, Fuqing, Chandra, Franciscus, Parisio, Giovanni, Chen, Hongjie, Xiao, Amy, Romeo, Claudia, Scali, Federico, Tonni, Matteo, Leifels, Mats, Chua, Feng Jun Desmond, Kwok, Germaine WC, Tay, Joey YR, Pasquali, Paolo, Thompson, Janelle, Alborali, Giovanni Loris, and Alm, Eric J

Published
2022
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7. Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis

Author

Veneri, C, Brandtner, D, Mancini, P, Bonanno Ferraro, G, Iaconelli, M, Suffredini, E, Petrillo, M, Leoni, G, Paracchini, V, Gawlik, B, Marchini, A, Torlontano, P, Aprea, G, Scattolini, S, Acciari, V, La Bianca, M, Cifarelli, R, Palma, A, Lauria, G, La Vecchia, G, Giordano, V, Cossentino, L, Pennino, F, Lombardi, A, Gentili, L, Angelini, P, Nasci, D, Alborali, G, Formenti, N, Guarneri, F, Fontani, N, Guercio, M, Mariuz, M, Trani, G, Pariani, A, De Lellis, L, Ancona, C, Barca, A, Serio, F, Giorgi, D, Ferrante, I, Capparuccini, V, Scicluna, M, Cersini, A, Pietrella, G, Nicosia, E, Grasselli, E, Izzotti, A, Tomesani, I, Bellisomi, M, Rosatto, S, Ammoni, E, Cereda, D, Bertasi, B, Losio, M, Oliva, D, Castiglioni, S, Schiarea, S, Binda, S, Primache, V, Pellegrinelli, L, Cocuzza, C, Musumeci, R, Bolognini, L, Filippetti, F, Paniccia', M, Briscolini, S, Magi, S, Grucci, A, Colitti, M, Ciccaglione, A, Montanaro, C, Griglio, B, Costa, A, Decastelli, L, Romano, A, Bianchi, M, Carraro, E, Pignata, C, Macrì, M, Bonetta, S, Albano, N, Di Vittorio, G, Mongelli, O, Apollonio, F, Triggiano, F, De Giglio, O, Montagna, M, Palermo, M, Maida, C, Mazzucco, W, Tramuto, F, De Grazia, S, Giammanco, G, Filizzolo, C, Purpari, G, Gucciardi, F, Ferrante, M, Agodi, A, Barchitta, M, Cala', P, Carducci, A, Verani, M, Federigi, I, Macrì, S, Federici, E, Petricciuolo, M, Carnevali, A, Russo, F, Pitter, G, Groppi, V, Rigoli, F, Zampini, M, Baldovin, T, Amoruso, I, Cadonna, M, Postinghel, M, Foladori, P, Zago, L, Stenico, A, Marco, M, Matteo, D, La Rosa, G, Veneri, C., Brandtner, D., Mancini, P., Bonanno Ferraro, G., Iaconelli, M., Suffredini, E., Petrillo, M., Leoni, G., Paracchini, V., Gawlik, B. M., Marchini, A., Torlontano, Paolo, Aprea, Giuseppe, Scattolini, Silvia, Acciari, Vicdalia Aniela, La Bianca, Michele, Cifarelli, Rosa Anna, Palma, Achille, Lauria, Giuseppe, La Vecchia, Giovanna, Giordano, Vincenzo, Cossentino, Luigi, Pennino, Francesca, Lombardi, Annalisa, Gentili, Lisa, Angelini, Paola, Nasci, Daniele, Alborali, Giovanni, Formenti, Nicoletta, Guarneri, Flavia, Fontani, Nadia, Guercio, Marco, Mariuz, Marika, Trani, Gabriella, Pariani, Anna, De Lellis, Laura, Ancona, Carla, Barca, Alessandra, Serio, Flavia, Giorgi, Doriana Antonella, Ferrante, Irene, Capparuccini, Valeria, Scicluna, Maria Teresa, Cersini, Antonella, Pietrella, Gabriele, Nicosia, Elena, Grasselli, Elena, Izzotti, Alberto, Tomesani, Irene, Bellisomi, Marta, Rosatto, Stefano, Ammoni, Emanuela, Cereda, Danilo, Bertasi, Barbara, Losio, Marina Nadia, Oliva, Desdemona, Castiglioni, Sara, Schiarea, Silvia, Binda, Sandro, Primache, Valeria, Pellegrinelli, Laura, Cocuzza, Clementina, Musumeci, Rosario, Bolognini, Luigi, Filippetti, Fabio, Paniccia', Marta, Briscolini, Sara, Magi, Silvia, Grucci, Annalisa, Colitti, Michele, Ciccaglione, Angela, Montanaro, Carmen, Griglio, Bartolomeo, Costa, Angela, Decastelli, Lucia, Romano, Angelo, Bianchi, Manila, Carraro, Elisabetta, Pignata, Cristina, Macrì, Manuela, Bonetta, Silvia, Albano, Nehludoff, Di Vittorio, Giuseppe, Mongelli, Onofrio, Apollonio, Francesca, Triggiano, Francesco, De Giglio, Osvalda, Montagna, Maria Teresa, Palermo, Mario, Maida, Carmelo Massimo, Mazzucco, Walter, Tramuto, Fabio, De Grazia, Simona, Giammanco, Giovanni Maurizio, Filizzolo, Chiara, Purpari, Giuseppa, Gucciardi, Francesca, Ferrante, Margherita, Agodi, Antonella, Barchitta, Martina, Cala', Piergiuseppe, Carducci, Annalaura, Verani, Marco, Federigi, Ileana, Macrì, Salvatore, Federici, Ermanno, Petricciuolo, Maya, Carnevali, Agnese, Russo, Francesca, Pitter, Gisella, Groppi, Vanessa, Rigoli, Franco, Zampini, Marco, Baldovin, Tatjana, Amoruso, Irene, Cadonna, Maria, Postinghel, Mattia, Foladori, Paola, Zago, Lorella, Stenico, Alberta, Marco, Morelli, Matteo, Dossena, La Rosa, G., Veneri, C, Brandtner, D, Mancini, P, Bonanno Ferraro, G, Iaconelli, M, Suffredini, E, Petrillo, M, Leoni, G, Paracchini, V, Gawlik, B, Marchini, A, Torlontano, P, Aprea, G, Scattolini, S, Acciari, V, La Bianca, M, Cifarelli, R, Palma, A, Lauria, G, La Vecchia, G, Giordano, V, Cossentino, L, Pennino, F, Lombardi, A, Gentili, L, Angelini, P, Nasci, D, Alborali, G, Formenti, N, Guarneri, F, Fontani, N, Guercio, M, Mariuz, M, Trani, G, Pariani, A, De Lellis, L, Ancona, C, Barca, A, Serio, F, Giorgi, D, Ferrante, I, Capparuccini, V, Scicluna, M, Cersini, A, Pietrella, G, Nicosia, E, Grasselli, E, Izzotti, A, Tomesani, I, Bellisomi, M, Rosatto, S, Ammoni, E, Cereda, D, Bertasi, B, Losio, M, Oliva, D, Castiglioni, S, Schiarea, S, Binda, S, Primache, V, Pellegrinelli, L, Cocuzza, C, Musumeci, R, Bolognini, L, Filippetti, F, Paniccia', M, Briscolini, S, Magi, S, Grucci, A, Colitti, M, Ciccaglione, A, Montanaro, C, Griglio, B, Costa, A, Decastelli, L, Romano, A, Bianchi, M, Carraro, E, Pignata, C, Macrì, M, Bonetta, S, Albano, N, Di Vittorio, G, Mongelli, O, Apollonio, F, Triggiano, F, De Giglio, O, Montagna, M, Palermo, M, Maida, C, Mazzucco, W, Tramuto, F, De Grazia, S, Giammanco, G, Filizzolo, C, Purpari, G, Gucciardi, F, Ferrante, M, Agodi, A, Barchitta, M, Cala', P, Carducci, A, Verani, M, Federigi, I, Macrì, S, Federici, E, Petricciuolo, M, Carnevali, A, Russo, F, Pitter, G, Groppi, V, Rigoli, F, Zampini, M, Baldovin, T, Amoruso, I, Cadonna, M, Postinghel, M, Foladori, P, Zago, L, Stenico, A, Marco, M, Matteo, D, La Rosa, G, Veneri, C., Brandtner, D., Mancini, P., Bonanno Ferraro, G., Iaconelli, M., Suffredini, E., Petrillo, M., Leoni, G., Paracchini, V., Gawlik, B. M., Marchini, A., Torlontano, Paolo, Aprea, Giuseppe, Scattolini, Silvia, Acciari, Vicdalia Aniela, La Bianca, Michele, Cifarelli, Rosa Anna, Palma, Achille, Lauria, Giuseppe, La Vecchia, Giovanna, Giordano, Vincenzo, Cossentino, Luigi, Pennino, Francesca, Lombardi, Annalisa, Gentili, Lisa, Angelini, Paola, Nasci, Daniele, Alborali, Giovanni, Formenti, Nicoletta, Guarneri, Flavia, Fontani, Nadia, Guercio, Marco, Mariuz, Marika, Trani, Gabriella, Pariani, Anna, De Lellis, Laura, Ancona, Carla, Barca, Alessandra, Serio, Flavia, Giorgi, Doriana Antonella, Ferrante, Irene, Capparuccini, Valeria, Scicluna, Maria Teresa, Cersini, Antonella, Pietrella, Gabriele, Nicosia, Elena, Grasselli, Elena, Izzotti, Alberto, Tomesani, Irene, Bellisomi, Marta, Rosatto, Stefano, Ammoni, Emanuela, Cereda, Danilo, Bertasi, Barbara, Losio, Marina Nadia, Oliva, Desdemona, Castiglioni, Sara, Schiarea, Silvia, Binda, Sandro, Primache, Valeria, Pellegrinelli, Laura, Cocuzza, Clementina, Musumeci, Rosario, Bolognini, Luigi, Filippetti, Fabio, Paniccia', Marta, Briscolini, Sara, Magi, Silvia, Grucci, Annalisa, Colitti, Michele, Ciccaglione, Angela, Montanaro, Carmen, Griglio, Bartolomeo, Costa, Angela, Decastelli, Lucia, Romano, Angelo, Bianchi, Manila, Carraro, Elisabetta, Pignata, Cristina, Macrì, Manuela, Bonetta, Silvia, Albano, Nehludoff, Di Vittorio, Giuseppe, Mongelli, Onofrio, Apollonio, Francesca, Triggiano, Francesco, De Giglio, Osvalda, Montagna, Maria Teresa, Palermo, Mario, Maida, Carmelo Massimo, Mazzucco, Walter, Tramuto, Fabio, De Grazia, Simona, Giammanco, Giovanni Maurizio, Filizzolo, Chiara, Purpari, Giuseppa, Gucciardi, Francesca, Ferrante, Margherita, Agodi, Antonella, Barchitta, Martina, Cala', Piergiuseppe, Carducci, Annalaura, Verani, Marco, Federigi, Ileana, Macrì, Salvatore, Federici, Ermanno, Petricciuolo, Maya, Carnevali, Agnese, Russo, Francesca, Pitter, Gisella, Groppi, Vanessa, Rigoli, Franco, Zampini, Marco, Baldovin, Tatjana, Amoruso, Irene, Cadonna, Maria, Postinghel, Mattia, Foladori, Paola, Zago, Lorella, Stenico, Alberta, Marco, Morelli, Matteo, Dossena, and La Rosa, G.

Abstract

The emergence of new SARS-CoV-2 variants poses challenges to global surveillance efforts, necessitating swift actions in their detection, evaluation, and management. Among the most recent variants, Omicron BA.2.86 and its sub-lineages have gained attention due to their potential immune evasion properties. This study describes the development of a digital PCR assay for the rapid detection of BA.2.86 and its descendant lineages, in wastewater samples. By using this assay, we analyzed wastewater samples collected in Italy from September 2023 to January 2024. Our analysis revealed the presence of BA.2.86 lineages already in October 2023 with a minimal detection rate of 2% which then rapidly increased, becoming dominant by January 2024, accounting for a prevalence of 62%. The findings emphasize the significance of wastewater-based surveillance in tracking emerging variants and underscore the efficacy of targeted digital PCR assays for environmental monitoring.

Published
2024

8. Regional-Scale Analysis of Antimicrobial Usage in Smallholder Cattle Herds (Aosta Valley, Italy):Why Surveillance Matters

Author

Scali, Federico, Ganio, Sandra, Roullet, Claudio, Ruffier, Mauro, Bergagna, Stefania, Pagliasso, Giulia, Romeo, Claudia, Formenti, Nicoletta, Maisano, Antonio Marco, Santucci, Giovanni, Tonni, Matteo, Guadagno, Federica, Mazza, Francesca, Guarneri, Flavia, Bontempi, Giorgio, Candela, Loredana, Alborali, Giovanni Loris, Scali, Federico, Ganio, Sandra, Roullet, Claudio, Ruffier, Mauro, Bergagna, Stefania, Pagliasso, Giulia, Romeo, Claudia, Formenti, Nicoletta, Maisano, Antonio Marco, Santucci, Giovanni, Tonni, Matteo, Guadagno, Federica, Mazza, Francesca, Guarneri, Flavia, Bontempi, Giorgio, Candela, Loredana, and Alborali, Giovanni Loris

Abstract

Optimising antimicrobial usage (AMU) in livestock is pivotal to counteract the emergence of antimicrobial resistance. We analysed AMU in more than 1000 cattle herds over 11 years (2008–2018) in the Aosta Valley (Italy), a region where 80% of farms house less than 50 cattle. Dairy cows accounted for over 95% of AMU. AMU was estimated using the defined daily dose animal for Italy (DDDAit) per biomass for the whole herd and a treatment incidence 100 (TI100) for cows. Average annual herd-level AMU was low, with 3.6 DDDAit/biomass (range: 3.2–4.0) and 1.2 TI100 in cows (range: 1.1–1.3). Third and fourth generation cephalosporins, which are critical for human medicine, represented almost 10% of usage, and intramammary antimicrobials accounted for over 60%. We detected significant downward temporal trends in total AMU, as well as a positive relationship with herd size. The magnitude of such effects was small, leaving scant room for further reduction. However, the frequent use of critical antimicrobials and intramammary products should be addressed, following the principles of prudent AMU. Our findings highlight the importance of monitoring AMU even in low-production, smallholding contexts where a low usage is expected, to identify any deficiencies and implement interventions for further AMU optimisation.

Published
2024

11. Regional-Scale Analysis of Antimicrobial Usage in Smallholder Cattle Herds (Aosta Valley, Italy): Why Surveillance Matters

Author

Scali, Federico, primary, Ganio, Sandra, additional, Roullet, Claudio, additional, Ruffier, Mauro, additional, Bergagna, Stefania, additional, Pagliasso, Giulia, additional, Romeo, Claudia, additional, Formenti, Nicoletta, additional, Maisano, Antonio Marco, additional, Santucci, Giovanni, additional, Tonni, Matteo, additional, Guadagno, Federica, additional, Mazza, Francesca, additional, Guarneri, Flavia, additional, Bontempi, Giorgio, additional, Candela, Loredana, additional, and Alborali, Giovanni Loris, additional

Published
2024
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12. Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Lee, Wei Lin, Armas, Federica, Guarneri, Flavia, Gu, Xiaoqiong, Formenti, Nicoletta, Wu, Fuqing, Chandra, Franciscus, Parisio, Giovanni, Chen, Hongjie, Xiao, Amy, Romeo, Claudia, Scali, Federico, Tonni, Matteo, Leifels, Mats, Chua, Feng Jun Desmond, Kwok, Germaine WC, Tay, Joey YR, Pasquali, Paolo, Thompson, Janelle, Alborali, Giovanni Loris, Alm, Eric J, Massachusetts Institute of Technology. Department of Biological Engineering, Lee, Wei Lin, Armas, Federica, Guarneri, Flavia, Gu, Xiaoqiong, Formenti, Nicoletta, Wu, Fuqing, Chandra, Franciscus, Parisio, Giovanni, Chen, Hongjie, Xiao, Amy, Romeo, Claudia, Scali, Federico, Tonni, Matteo, Leifels, Mats, Chua, Feng Jun Desmond, Kwok, Germaine WC, Tay, Joey YR, Pasquali, Paolo, Thompson, Janelle, Alborali, Giovanni Loris, and Alm, Eric J

Abstract

On November 26, 2021, the B.1.1.529 COVID-19 variant was classified as the Omicron variant of concern (VOC). Reports of higher transmissibility and potential immune evasion triggered flight bans and heightened health control measures across the world to stem its distribution. Wastewater-based surveillance has demonstrated to be a useful complement for clinical community-based tracking of SARS-CoV-2 variants. Using design principles of our previous assays that detect SARS-CoV-2 variants (Alpha and Delta), we developed an allele-specific RT-qPCR assay which simultaneously targets the stretch of mutations from Q493R to Q498R for quantitative detection of the Omicron variant in wastewater. We report their validation against 10-month longitudinal samples from the influent of a wastewater treatment plant in Italy. SARS-CoV-2 RNA concentrations and variant frequencies in wastewater determined using these variant assays agree with clinical cases, revealing rapid displacement of the Delta variant by the Omicron variant within three weeks. These variant trends, when mapped against vaccination rates, support clinical studies that found the rapid emergence of SARS-CoV-2 Omicron variant being associated with an infection advantage over Delta in vaccinated persons. These data reinforce the versatility, utility and accuracy of these open-sourced methods using allele-specific RT-qPCR for tracking the dynamics of variant displacement in communities through wastewater for informed public health responses.

Published
2023

13. Wastewater surveillance of SARS-CoV-2 variants in October–November 2022 in Italy: detection of XBB.1, BA.2.75 and rapid spread of the BQ.1 lineage

Author

La Rosa, G., primary, Brandtner, D., additional, Bonanno Ferraro, G., additional, Veneri, C., additional, Mancini, P., additional, Iaconelli, M., additional, Lucentini, L., additional, Del Giudice, C., additional, Orlandi, L., additional, Suffredini, E., additional, Palma, Achille, additional, Calabria, Adelaide, additional, Carnevali, Agnese, additional, Nehludoff, Albano, additional, Stenico, Alberta, additional, Izzotti, Alberto, additional, Barca, Alessandra, additional, Tosco, Alessandra, additional, Porta, Amalia, additional, Lombardi, Annalisa, additional, Voli, Antonia, additional, Franzetti, Andrea, additional, Ciccaglione, Angela, additional, Costa, Angela, additional, D’Argenzio, Angelo, additional, Romano, Angelo, additional, Pariani, Anna, additional, Carducci, Annalaura, additional, Grucci, Annalisa, additional, Prast, Anna-Maria, additional, Agodi, Antonella, additional, Cersini, Antonella, additional, Giorgi, Antonella, additional, Bertasi, Barbara, additional, Griglio, Bartolomeo, additional, Ancona, Carla, additional, Maida, Carmelo Massimo, additional, Montanaro, Carmen, additional, Filizzolo, Chiara, additional, Ottaviano, Claudio, additional, Cocuzza, Clementina, additional, Pignata, Cristina, additional, Nasci, Daniele, additional, Cereda, Danilo, additional, Oliva, Desdemona, additional, Giorgi, Doriana Antonella, additional, Malacaria, Edoardo, additional, Grasselli, Elena, additional, Nicosia, Elena, additional, Carraro, Elisabetta, additional, Ammoni, Emanuela, additional, Grange, Eric, additional, Federici, Ermanno, additional, Filippetti, Fabio, additional, Tramuto, Fabio, additional, Guarneri, Flavia, additional, Serio, Flavia, additional, Damasco, Florida, additional, Palumbo, Franca, additional, Apollonio, Francesca, additional, Cutrupi, Francesca, additional, Gucciardi, Francesca, additional, Pennino, Francesca, additional, Russo, Francesca, additional, Triggiano, Francesco, additional, Rigoli, Franco, additional, Pietrella, Gabriele, additional, Trani, Gabriella, additional, Rossolini, Gian Maria, additional, Bulotta, Giorgia, additional, Fusco, Giovanna, additional, La Vecchia, Giovanna, additional, Alborali, Giovanni, additional, Giammanco, Giovanni, additional, Santoro, Giovanni, additional, Pitter, Gisella, additional, Purpari, Giuseppa, additional, Aprea, Giuseppe, additional, Di Vittorio, Giuseppe, additional, Folino, Giuseppe, additional, Lauria, Giuseppe, additional, Federigi, Ileana, additional, Amoruso, Irene, additional, Ferrante, Irene, additional, Tomesani, Irene, additional, De Lellis, Laura, additional, Pellegrinelli, Laura, additional, Demetz, Lea, additional, Gentili, Lisa, additional, Richiardi, Lisa, additional, Zago, Lorella, additional, Masieri, Lorena, additional, Decastelli, Lucia, additional, Bolognini, Luigi, additional, Cossentino, Luigi, additional, Bianchi, Manila, additional, Verani, Marco, additional, Zampini, Marco, additional, Ferrante, Margherita, additional, Cadonna, Maria, additional, Montagna, Maria Teresa, additional, Scicluna, Maria Teresa, additional, Arizzi, Mariaconcetta, additional, Mariuz, Marika, additional, Palermo, Mario, additional, Bellisomi, Marta, additional, Paniccià, Marta, additional, Barchitta, Martina, additional, Ramazzotti, Matteo, additional, Postinghel, Mattia, additional, Viscardi, Maurizio, additional, Ruffier, Mauro, additional, Petricciuolo, Maya, additional, La Bianca, Michele, additional, Colitti, Michele, additional, Monfrinotti, Monica, additional, Fontani, Nadia, additional, Formenti, Nicoletta, additional, Mongelli, Onofrio, additional, De Giglio, Osvalda, additional, Angelini, Paola, additional, Foladori, Paola, additional, Torlontano, Paolo, additional, Calà, Piergiuseppe, additional, Cifarelli, Rosa Anna, additional, Binda, Sandro, additional, Briscolini, Sara, additional, Castiglioni, Sara, additional, Bonetta, Silvia, additional, Magi, Silvia, additional, Scattolini, Silvia, additional, Schiarea, Silvia, additional, De Grazia, Simona, additional, Rosatto, Stefano, additional, Baldovin, Tatjana, additional, Primache, Valeria, additional, Groppi, Vanessa, additional, Acciari, Vicdalia Aniela, additional, and Mazzucco, Walter, additional

Published
2023
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14. The hazard of carbapenemase (OXA-181)-producing Escherichia coli spreading in pig and veal calf holdings in Italy in the genomics era: Risk of spill over and spill back between humans and animals

Author

Carfora, Virginia, primary, Diaconu, Elena Lavinia, additional, Ianzano, Angela, additional, Di Matteo, Paola, additional, Amoruso, Roberta, additional, Dell'Aira, Elena, additional, Sorbara, Luigi, additional, Bottoni, Francesco, additional, Guarneri, Flavia, additional, Campana, Laura, additional, Franco, Alessia, additional, Alba, Patricia, additional, and Battisti, Antonio, additional

Published
2022
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15. The rapid spread of SARS-COV-2 Omicron variant in Italy reflected early through wastewater surveillance

Author

La Rosa, G., primary, Iaconelli, M., additional, Veneri, C., additional, Mancini, P., additional, Bonanno Ferraro, G., additional, Brandtner, D., additional, Lucentini, L., additional, Bonadonna, L., additional, Rossi, M., additional, Grigioni, M., additional, Suffredini, E., additional, Palma, Achille, additional, Stenico, Alberta, additional, Antonelli, Alberto, additional, Izzotti, Alberto, additional, Schiavuzzi, Alessandra, additional, Tosco, Alessandra, additional, Porta, Amalia, additional, Franzetti, Andrea, additional, Turolla, Andrea, additional, Costa, Angela, additional, D’Argenzio, Angelo, additional, Romano, Angelo, additional, Pariani, Anna, additional, Carducci, Annalaura, additional, Prast, Anna-Maria, additional, Agodi, Antonella, additional, Cersini, Antonella, additional, Pizzolante, Antonio, additional, Azzellino, Arianna, additional, Bertasi, Barbara, additional, Griglio, Bartolomeo, additional, Ancona, Carla, additional, Maida, Carmelo Massimo, additional, Montanaro, Carmen, additional, Ottaviano, Claudio, additional, Cocuzza, Clementina, additional, Pignata, Cristina, additional, Nasci, Daniele, additional, Cereda, Danilo, additional, Oliva, Desdemona, additional, Giorgi, Doriana Antonella, additional, Grasselli, Elena, additional, Mengon, Elena, additional, Nicosia, Elena, additional, Carraro, Elisabetta, additional, Ammoni, Emanuela, additional, Ricci, Enrica, additional, Grange, Eric, additional, Federici, Ermanno, additional, Zuccato, Ettore, additional, Filippetti, Fabio, additional, Zuccon, Fabio, additional, Guarneri, Flavia, additional, Damasco, Florida, additional, Palumbo, Franca, additional, Apollonio, Francesca, additional, Borney, Francesca, additional, Ciuti, Francesca, additional, Cutrupi, Francesca, additional, Malpei, Francesca, additional, Pennino, Francesca, additional, Russo, Francesca, additional, Pizzo, Francesco, additional, Triggiano, Francesco, additional, Rigoli, Franco, additional, Trani, Gabriella, additional, Cecchini, Giancarlo, additional, Borlone, Gianluca, additional, Allaria, Giorgia, additional, Bertanza, Giorgio, additional, Fusco, Giovanna, additional, La Vecchia, Giovanna, additional, Alborali, Giovanni, additional, Giammanco, Giovanni, additional, Santoro, Giovanni, additional, Pitter, Gisella, additional, Lauretani, Giulia, additional, Nani, Giulia, additional, Purpari, Giuseppa, additional, Aprea, Giuseppe, additional, Bucciarelli, Giuseppe, additional, Di Vittorio, Giuseppe, additional, Lauria, Giuseppe, additional, Federigi, Ileana, additional, Amoruso, Irene, additional, Ferrante, Irene, additional, De Lellis, Laura, additional, Gentili, Lisa, additional, Zago, Lorella, additional, Decastelli, Lucia, additional, Bolognini, Luigi, additional, Cossentino, Luigi, additional, Bianchi, Manila, additional, Antonelli, Manuela, additional, Guercio, Marco, additional, Verani, Marco, additional, Zampini, Marco, additional, Ferrante, Margherita, additional, Cadonna, Maria, additional, Cerroni, Maria Grazia, additional, Callegari, Maria Luisa, additional, Montagna, Maria Teresa, additional, Scicluna, Maria Teresa, additional, Arizzi, Mariaconcetta, additional, Mariuz, Marika, additional, Losio, Marina Nadia, additional, Palermo, Mario, additional, Paniccià, Marta, additional, Triassi, Maria, additional, Barchitta, Martina, additional, Ramazzotti, Matteo, additional, Postinghel, Mattia, additional, Cravero, Mauro, additional, Ruffier, Mauro, additional, Petricciuolo, Maya, additional, La Bianca, Michele, additional, Colitti, Michele, additional, Monfrinotti, Monica, additional, Fontani, Nadia, additional, Ungaro, Nicola, additional, Formenti, Nicoletta, additional, Mongelli, Onofrio, additional, De Giglio, Osvalda, additional, Angelini, Paola, additional, Foladori, Paola, additional, Torlontano, Paolo, additional, Montenegro, Patrizia, additional, Laura, Pellegrinelli, additional, Calà, Piergiuseppe, additional, Olivares, Renato, additional, Berruti, Renza, additional, Cifarelli, Rosa Anna, additional, Brienza, Rosanna, additional, Binda, Sandro, additional, Briscolini, Sara, additional, Castiglioni, Sara, additional, Muzio, Sara, additional, Manara, Serena, additional, Bonetta, Silvia, additional, Magi, Silvia, additional, Riosa, Silvia, additional, Schiarea, Silvia, additional, De Grazia, Simona, additional, Barigelli, Sofia, additional, Rosatto, Stefano, additional, Baldovin, Tatjana, additional, Capparuccini, Valeria, additional, Primache, Valeria, additional, Groppi, Vanessa, additional, and Mazzucco, Walter, additional

Published
2022
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16. PRRS Monitoring by Processing Fluids on Italian Swine Breeding Farms.

Author

Tonni, Matteo, Romeo, Claudia, Formenti, Nicoletta, Boniotti, Maria Beatrice, Guarneri, Flavia, Colosio, Livio, Andreoni, Simone, Scali, Federico, and Alborali, Giovanni Loris

Subjects
SWINE breeds, SWINE farms, PORCINE reproductive & respiratory syndrome, SWINE breeding, BLOOD serum analysis
Abstract

Simple Summary: Processing fluids (PFs) are novel diagnostic specimens consisting of serosanguineous exudate obtained from tissues after piglets' castration. PFs can be used for some diagnostic tests that would otherwise require a blood sample. This has the advantage of not subjecting piglets to an additional stressful procedure and, at the same time, reducing sampling costs. In the present study, the efficacy and reliability of a monitoring plan for porcine reproductive and respiratory syndrome (PRRS), one of the main pig diseases, based on PF sampling has been assessed in the Italian swine production system. Twenty-five breeding herds were monitored for 4–5 months by RT-PCR performed on both PFs and blood serum (the standard specimen used for monitoring). Based on the results obtained from each method, the herds were classified following the standard PRRS status categories. The two methods fully agreed in discriminating between herds with stable and unstable PRRSV circulation. However, we observed a slight discrepancy in classifying high- and low-prevalence herds within unstable herds. We conclude that PFs are a reliable material for the PRRSV surveillance and classification of breeding herds, but in case of unstable circulation, a strategy combining blood and PF sampling is recommended. The porcine reproductive and respiratory syndrome (PRRS) control strategy within swine breeding farms is based on herd classification relative to PRRSV infection status. This study aims to assess the efficacy of a monitoring plan based on processing fluids (PFs) by comparing it with the classification of herds based on the analysis of blood serum. Twenty-five breeding herds were enrolled in the study, with at least five consecutive batches sampled from each herd. Each batch was tested for PRRSV by RT-PCR performed on (i) pre-weaning blood serum from 30 piglets and (ii) PFs from all the male piglets in the batch. PRRS categories following the Holtkamp classification were assigned based on the results of each testing protocol. The two protocols assigned the same category to 18 out of 25 herds: while they showed perfect agreement in identifying positive unstable and stable herds, we observed some discrepancy in discriminating between low- and high-prevalence classes within unstable herds. PFs are thus a reliable sample to assign PRRS categories in Italian breeding herds characterized by widespread PRRSV circulation. However, in case of an unstable epidemiological scenario, we recommend the adoption of an integrated monitoring strategy that combines blood sampling with PFs. [ABSTRACT FROM AUTHOR]

Published
2023
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17. Additional file 1 of The role of co-infections in M. hyopneumoniae outbreaks among heavy fattening pigs: a field study

Author

Tonni, Matteo, Formenti, Nicoletta, Boniotti, M. Beatrice, Guarneri, Flavia, Scali, Federico, Romeo, Claudia, Pasquali, Paolo, Pieters, Maria, Maes, Dominiek, and Alborali, Giovanni L.

Subjects
mental disorders, bacteria, bacterial infections and mycoses
Abstract

Additional file 1. Allele calling table. Each VNTR type is identified as a combination of different VNTR locus. The number of repeats of each locus is determined by the number of base pairs (bp) for that locus.

Published
2022
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18. First Detection of mcr-9 in a Multidrug-Resistant Escherichia coli of Animal Origin in Italy Is Not Related to Colistin Usage on a Pig Farm.

Author

Guarneri, Flavia, Bertasio, Cristina, Romeo, Claudia, Formenti, Nicoletta, Scali, Federico, Parisio, Giovanni, Canziani, Sabrina, Boifava, Chiara, Guadagno, Federica, Boniotti, Maria Beatrice, and Alborali, Giovanni Loris

Subjects
SWINE farms, GRAM-negative bacterial diseases, COLISTIN, ESCHERICHIA coli, WHOLE genome sequencing, GENE targeting
Abstract

The emergence of colistin resistance raises growing concerns because of its use as a last-resort antimicrobial for the treatment of severe gram-negative bacterial infections in humans. Plasmid-borne mobile colistin resistance genes (mcr) are particularly worrisome due to their high propensity to spread. An mcr-9-positive Escherichia coli was isolated from a piglet in Italy, representing the first isolation of this gene from an E. coli of animal origin in the country. Whole genome sequencing (WGS) revealed that mcr-9 was borne by an IncHI2 plasmid carrying several other resistance genes. The strain was indeed phenotypically resistant to six different antimicrobial classes, including 3rd and 4th generation cephalosporins. Despite the presence of mcr-9, the isolate was susceptible to colistin, probably because of a genetic background unfavourable to mcr-9 expression. The lack of colistin resistance, coupled with the fact that the farm of origin had not used colistin in years, suggests that mcr-9 in such a multidrug-resistant strain can be maintained thanks to the co-selection of neighbouring resistance genes, following usage of different antimicrobials. Our findings highlight how a comprehensive approach, integrating phenotypical testing, targeted PCR, WGS-based techniques, and information on antimicrobial usage is crucial to shed light on antimicrobial resistance. [ABSTRACT FROM AUTHOR]

Published
2023
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20. Extended-Spectrum-β-Lactamase- and AmpC-Producing Escherichia coli in Domestic Dogs: Spread, Characterisation and Associated Risk Factors

Author

Formenti, Nicoletta, primary, Grassi, Andrea, additional, Parisio, Giovanni, additional, Romeo, Claudia, additional, Guarneri, Flavia, additional, Birbes, Laura, additional, Pitozzi, Alessandra, additional, Scali, Federico, additional, Maisano, Antonio Marco, additional, Boniotti, Maria Beatrice, additional, Pasquali, Paolo, additional, and Alborali, Giovanni Loris, additional

Published
2021
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22. Additional file 1 of Genomic variability of Mycoplasma hyopneumoniae within pig lung lobes

Author

Tonni, Matteo, M. Beatrice Boniotti, Gasparrini, Sara, Guarneri, Flavia, Formenti, Nicoletta, Pieters, Maria, Pasquali, Paolo, and Alborali, Giovanni L.

Subjects
mental disorders, bacteria, bacterial infections and mycoses
Abstract

Additional file 1: Table 1. Allele calling table. Each VNTR type is identified as a combination of different VNTR locus. The number of repeats of each locus is determinate by the number of base pair (bp) for that locus.

Published
2021
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23. Antimicrobial Resistance of Escherichia coli in Dairy Calves: A 15-Year Retrospective Analysis and Comparison of Treated and Untreated Animals

Author

Formenti, Nicoletta, primary, Martinelli, Chiara, additional, Vitale, Nicoletta, additional, Giovannini, Stefano, additional, Salogni, Cristian, additional, Tonni, Matteo, additional, Scali, Federico, additional, Birbes, Laura, additional, D’Incau, Mario, additional, Guarneri, Flavia, additional, Pasquali, Paolo, additional, and Alborali, Giovanni Loris, additional

Published
2021
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24. ESBL/AmpC-Producing Escherichia coli in Wild Boar: Epidemiology and Risk Factors

Author

Formenti, Nicoletta, primary, Calò, Stefania, additional, Parisio, Giovanni, additional, Guarneri, Flavia, additional, Birbes, Laura, additional, Pitozzi, Alessandra, additional, Scali, Federico, additional, Tonni, Matteo, additional, Guadagno, Federica, additional, Giovannini, Stefano, additional, Salogni, Cristian, additional, Ianieri, Adriana, additional, Bellini, Silvia, additional, Pasquali, Paolo, additional, and Alborali, Giovanni Loris, additional

Published
2021
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27. Analysis of the Comparative Occurrence of Salmonella Typhimurium and Its Monophasic Variant (4,[5],12:i:-) in Healthy and Clinically Ill Pigs in Northern Italy

Author

D'Incau, Mario, primary, Salogni, Cristian, additional, Giovannini, Stefano, additional, Ruggeri, Jessica, additional, Scali, Federico, additional, Tonni, Matteo, additional, Formenti, Nicoletta, additional, Guarneri, Flavia, additional, Pasquali, Paolo, additional, and Alborali, Giovanni Loris, additional

Published
2020
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28. In vitro Cytokine Responses to Virulent PRRS Virus Strains

Author

Ferlazzo, Gianluca, primary, Ruggeri, Jessica, additional, Boniotti, Maria Beatrice, additional, Guarneri, Flavia, additional, Barbieri, Ilaria, additional, Tonni, Matteo, additional, Bertasio, Cristina, additional, Alborali, Giovanni Loris, additional, and Amadori, Massimo, additional

Published
2020
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30. Occurrence of Salmonella Typhimurium and its monophasic variant (4, [5],12:i:-) in healthy and clinically ill pigs in northern Italy.

Author

D'Incau, Mario, Salogni, Cristian, Giovannini, Stefano, Ruggeri, Jessica, Scali, Federico, Tonni, Matteo, Formenti, Nicoletta, Guarneri, Flavia, Pasquali, Paolo, and Alborali, Giovanni Loris

Subjects
SALMONELLA typhimurium, SALMONELLA diseases, SEROTYPES, EPIDEMIOLOGY
Abstract

Background: The serovar Typhimurium (4, [5],12:i:1,2), is the most frequently isolated serovar in case of salmonellosis in pigs in Europe and its monophasic variant (4, [5],12:i:-) has been increasingly responsible for Salmonella outbreaks in humans. A total of 25,215 samples were collected, during the years 2002–2017, from 1359 pig farms located in Northern Italy. Samples were collected from different material sources including fecal samples, rectal swabs, gut content and different organs. Results: Salmonella was isolated in 15.80% of samples and, among the isolates, 733 were typed as Salmonella Typhimurium (ST) or its monophasic variant (MST). Over time, there was an increase of isolation of MST which outnumbered ST. Most of the strains were isolated in animals during the weaning stage and the growing – fattening period whereas the clinical cases were mainly present in young pigs after weaning. Conclusions: This study confirms the presence of ST and MST in pig farms although, considering the total of isolated serotypes, with lower percentages than previously reported. In the last few years, ST has increasingly been replaced by MST suggesting that MST has a competitive advantage over ST, probably due to its different antigenicity and pathogenicity which renders the infection stealthier to recognize and control. [ABSTRACT FROM AUTHOR]

Published
2021
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