130 results on '"Sá-Leão, R."'
Search Results
2. High invasiveness of pneumococcal serotypes included in the new generation of conjugate vaccines
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del Amo, E., Brotons, P., Monsonis, M., Trivióo, M., Ióigo, M., Selva, L., Sa-Leão, R., and Muóoz-Almagro, C.
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- 2014
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3. Prevalence, risk factors, and epidemiology of methicillin-resistantStaphylococcus aureus carried by adults over 60 years of age
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Almeida, S. T., Nunes, S., Paulo, A. C. S., Faria, N. A., de Lencastre, H., and Sá-Leão, R.
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- 2015
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4. Characteristics of Haemophilus influenzae invasive isolates from Portugal following routine childhood vaccination against H. influenzae serotype b (2002–2010)
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Bajanca-Lavado, M. P., Simões, A. S., Betencourt, C. R., Sá-Leão, R., and The Portuguese Group for the Study of Haemophilus influenzae invasive infection
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- 2014
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5. Changes in pneumococcal serotypes and antibiotypes carried by vaccinated and unvaccinated day-care centre attendees in Portugal, a country with widespread use of the seven-valent pneumococcal conjugate vaccine
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Sá-Leão, R., Nunes, S., Brito-Avô, A., Frazão, N., Simões, A.S., Crisóstomo, M.I., Paulo, A.C.S., Saldanha, J., Santos-Sanches, I., and de Lencastre, H.
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- 2009
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6. Streptococcus Pneumoniae Evolving – Impact of Antibiotics and Vaccines☆
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Sá-Leão, R., primary and Tomasz, A., additional
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- 2014
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- View/download PDF
7. Carriage of multiple Streptococcus pneumoniae capsular types is frequent among children with invasive pneumococcal disease
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Félix S, Henares-Bonilla D, Munoz-Almagro C, and Sá-Leão R
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Co-colonization ,Streptococcus pneumoniae ,Invasive pneumococcal disease ,Multiple serotype carriage ,Children - Abstract
Streptococcus pneumoniae (pneumococcus) is a human pathogen that colonizes the nasopharynx. We investigated serotype distribution in paired invasive and nasopharyngeal samples obtained from 57 children during invasive pneumococcal disease. Of 39 nasopharyngeal samples positive for pneumococci, 46.2% contained a serotype different from the one causing disease. This study reports a high frequency of pneumococcal multiple serotype carriage in children with invasive pneumococcal disease. Whether multiple serotype carriage is important for the onset and progress to pneumococcal infection warrants further investigation.
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- 2021
8. Emergence of a serotype 1 Streptococcus pneumoniae lineage colonising healthy children in Portugal in the seven-valent conjugate vaccination era
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Nunes, S., Sá-Leão, R., Pereira, L.C., and de Lencastre, H.
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- 2008
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9. Upper airways colonisation of Streptococcus pneumoniae in adults aged 60 years and older: A systematic review of prevalence and individual participant data meta-analysis of risk factors
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Smith, EL, Wheeler, I, Adler, H, Ferreira, DM, Sá-Leão, R, Abdullahi, O, Adetifa, I, Becker-Dreps, S, Esposito, S, Farida, H, Kandasamy, R, Mackenzie, GA, Nuorti, JP, Nzenze, S, Madhi, SA, Ortega, O, Roca, A, Safari, D, Schaumburg, F, Usuf, E, Sanders, EAM, Grant, LR, Hammitt, LL, O'Brien, KL, Gounder, P, Bruden, DJT, Stanton, MC, Rylance, J, Smith, EL, Wheeler, I, Adler, H, Ferreira, DM, Sá-Leão, R, Abdullahi, O, Adetifa, I, Becker-Dreps, S, Esposito, S, Farida, H, Kandasamy, R, Mackenzie, GA, Nuorti, JP, Nzenze, S, Madhi, SA, Ortega, O, Roca, A, Safari, D, Schaumburg, F, Usuf, E, Sanders, EAM, Grant, LR, Hammitt, LL, O'Brien, KL, Gounder, P, Bruden, DJT, Stanton, MC, and Rylance, J
- Abstract
Background: Colonisation with Streptococcus pneumoniae can lead to invasive pneumococcal disease and pneumonia. Pneumococcal acquisition and prevalence of colonisation are high in children. In older adults, a population susceptible to pneumococcal disease, colonisation prevalence is reported to be lower, but studies are heterogeneous. Methods: This is a systematic review and meta-analysis of prevalence of, and risk factors for, pneumococcal colonisation in adults ≥ 60 years of age (PROSPERO #42016036891). We identified peer-reviewed studies reporting the prevalence of S. pneumoniae colonisation using MEDLINE and EMBASE (until April 2016), excluding studies of acute disease. Participant-level data on risk factors were sought from each study. Findings: Of 2202 studies screened, 29 were analysable: 18 provided participant-level data (representing 6290 participants). Prevalence of detected pneumococcal colonisation was 0–39% by conventional culture methods and 3–23% by molecular methods. In a multivariate analysis, colonisation was higher in persons from nursing facilities compared with the community (odds ratio (OR) 2•30, 95% CI 1•26–4•21 and OR 7•72, 95% CI 1•15–51•85, respectively), in those who were currently smoking (OR 1•69, 95% CI 1•12–2•53) or those who had regular contact with children (OR 1•93, 95%CI 1•27–2•93). Persons living in urban areas had significantly lower carriage prevalence (OR 0•43, 95%CI 0•27–0•70). Interpretation: Overall prevalence of pneumococcal colonisation in older adults was higher than expected but varied by risk factors. Future studies should further explore risk factors for colonisation, to highlight targets for focussed intervention such as pneumococcal vaccination of high-risk groups. Funding: No funding was required.
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- 2020
10. Upper airways colonisation of Streptococcus pneumoniae in adults aged 60 years and older:A systematic review of prevalence and individual participant data meta-analysis of risk factors
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Smith, E.L., Wheeler, I., Adler, H., Ferreira, D.M., Sá-Leão, R., Abdullahi, O., Adetifa, I., Becker-Dreps, S., Esposito, S., Farida, H., Kandasamy, R., Mackenzie, G.A., Nuorti, J.P., Nzenze, S., Madhi, S.A., Ortega, O., Roca, A., Safari, D., Schaumburg, F., Usuf, E., Sanders, E.A.M., Grant, L.R., Hammitt, L.L., O'Brien, K.L., Gounder, P., Bruden, D.J.T., Stanton, M.C., Rylance, J., Smith, E.L., Wheeler, I., Adler, H., Ferreira, D.M., Sá-Leão, R., Abdullahi, O., Adetifa, I., Becker-Dreps, S., Esposito, S., Farida, H., Kandasamy, R., Mackenzie, G.A., Nuorti, J.P., Nzenze, S., Madhi, S.A., Ortega, O., Roca, A., Safari, D., Schaumburg, F., Usuf, E., Sanders, E.A.M., Grant, L.R., Hammitt, L.L., O'Brien, K.L., Gounder, P., Bruden, D.J.T., Stanton, M.C., and Rylance, J.
- Abstract
Background: Colonisation with Streptococcus pneumoniae can lead to invasive pneumococcal disease and pneumonia. Pneumococcal acquisition and prevalence of colonisation are high in children. In older adults, a population susceptible to pneumococcal disease, colonisation prevalence is reported to be lower, but studies are heterogeneous. Methods: This is a systematic review and meta-analysis of prevalence of, and risk factors for, pneumococcal colonisation in adults ≥ 60 years of age (PROSPERO #42016036891). We identified peer-reviewed studies reporting the prevalence of S. pneumoniae colonisation using MEDLINE and EMBASE (until April 2016), excluding studies of acute disease. Participant-level data on risk factors were sought from each study. Findings: Of 2202 studies screened, 29 were analysable: 18 provided participant-level data (representing 6290 participants). Prevalence of detected pneumococcal colonisation was 0–39% by conventional culture methods and 3–23% by molecular methods. In a multivariate analysis, colonisation was higher in persons from nursing facilities compared with the community (odds ratio (OR) 2•30, 95% CI 1•26–4•21 and OR 7•72, 95% CI 1•15–51•85, respectively), in those who were currently smoking (OR 1•69, 95% CI 1•12–2•53) or those who had regular contact with children (OR 1•93, 95%CI 1•27–2•93). Persons living in urban areas had significantly lower carriage prevalence (OR 0•43, 95%CI 0•27–0•70). Interpretation: Overall prevalence of pneumococcal colonisation in older adults was higher than expected but varied by risk factors. Future studies should further explore risk factors for colonisation, to highlight targets for focussed intervention such as pneumococcal vaccination of high-risk groups. Funding: No funding was required. © 2020
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- 2020
11. Streptococcus Pneumoniae
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Sá-Leão, R., primary and Tomasz, A., additional
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- 2009
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12. Penicillin resistance caused by dissemination of serotype 14 - clone Spain9V ST156 in the vaccine era: O494
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Simões, A. S., Sá-Leão, R., Nunes, S., Frazão, N., Tavares, A., and de Lencastre, H.
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- 2009
13. Invasive disease potential of pneumococcal clones carried by children: S46
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de Lencastre, H., Sá-Leão, R., Ramirez, M., and Melo-Cristino, J.
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- 2007
14. Serotype 11A prevalence and clonal diversity in Streptococcus pneumoniae isolated from children attending daycare centres in Lisbon, Portugal: P1020
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Sousa, N. G., Nunes, S., Frazão, N., Sá-Leão, R., and de Lencastre, H.
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- 2005
15. Effect of the 7-valent conjugate pneumococcal vaccine on the serotype distribution of drug-susceptible and drug-resistant Streptococcus pneumoniae colonising healthy children attending day-care centres in Lisbon: P618
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Frazão, N., Nunes, S., Sousa, N. G., Sá-Leão, R., Simas, C., Mato, R., Brito-Avô, A., Saldanha, J., Santos-Sanches, I., and de Lencastre, H.
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- 2005
16. Prevalence of non-typeable Streptococcus pneumoniae in carriers and insights into its population structure: O213
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Sá-Leão, R., Simoes, A., Nunes, S., Sousa, N. G., Frazao, N., and de Lencastre, H.
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- 2005
17. ACKNOWLEDGEMENT OF REVIEWERS
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Adams, NG, Adekambi, T, Afeltra, J, Aguado, J, Aires de Sousa, M, Akiyoshi, K, Al Hasan, M, Ala-Kokko, T, Albert, M, Alfandari, S, Allen, D, Allerberger, F, Almyroudis, N, Alp, E, Amin, R, Anderson-Berry, A, Andes, DR, Andremont, A, Andreu, A, Angelakis, M, Antachopoulos, C, Antoniadou, A, Arabatzis, M, Arlet, G, Arnez, M, Arnold, C, Asensio, A, Asseray, N, Ausiello, C, Avni, T, Ayling, R, Baddour, L, Baguelin, M, Bányai, K, Barbour, A, Basco, LK, Bauer, D, Bayston, R, Beall, B, Becker, K, Behr, M, Bejon, P, Belliot, G, Benito-Fernandez, J, Benjamin, D, Benschop, K, Berencsi, G, Bergeron, MG, Bernard, K, Berner, R, Beyersmann, J, Bille, J, Bizzini, A, Bjarnsholt, T, Blanc, D, Blanco, J, Blot, S, Bohnert, J, Boillat, N, Bonomo, R, Bonten, M, Bordon, JM, Borel, N, Boschiroli, ML, Bosilkovski, M, Bosso, JA, Botelho-Nevers, E, Bou, G, Bretagne, S, Brouqui, P, Brun-Buisson, C, Brunetto, M, Bucher, H, Buchheidt, D, Buckling, A, Bulpa, P, Cambau, E, Canducci, F, Cantón, R, Capobianchi, M, Carattoli, A, Carcopino, X, Cardona-Castro, N, Carling, PC, Carrat, F, Castilla, J, Castilletti, C, Cavaco, L, Cavallo, R, Ceccherini-Silberstein, F, Centrón, D, Chappuis, F, Charrel, R, Chen, M, Chevaliez, S, Chezzi, C, Chomel, B, Chowers, M, Chryssanthou, E, Ciammaruconi, A, Ciccozzi, M, Cid, J, Ciofu, O, Cisneros, D, Ciufolini, MG, Clark, C, Clarke, SC, Clayton, R, Clementi, M, Clemons, K, Cloeckaert, Ael, Cloud, J, Coenye, T, Cohen Bacri, S, Cohen, R, Coia, J, Colombo, A, Colson, P, Concerse, P, Cordonnier, C, Cormican, M, Cornaglia, G, Cornely, O, Costa, S, Cots, F, Craxi, A, Creti, R, Crnich, C, Cuenca Estrella, M, Cusi, MG, d'Ettorre, G, da Cruz Lamas, C, Daikos, G, Dannaoui, E, De Barbeyrac, B, De Grazia, S, de Jager, C, de Lamballerie, X, de Marco, F, del Palacio, A, Delpeyroux, F, Denamur, E, Denis, O, Depaquit, J, Deplano, A, Desenclos, J-C, Desjeux, P, Deutch, S, Di Luca, D, Dianzani, F, Diep, B, Diestra, K, Dignani, C, Dimopoulos, G, Divizia, M, Doi, Y, Dornbusch, HJ, Dotis, J, Drancourt, M, Drevinek, P, Dromer, F, Dryden, M, Dubreuil, L, Dubus, J-C, Dumitrescu, O, Dumke, R, DuPont, H, Edelstein, M, Eggimann, P, Eis-Huebinger, A-M, El Atrouni, WI, Entenza, J, Ergonul, O, Espinel-Ingroff, A, Esteban, J, Etienne, J, Fan, X-G, Fenollar, F, Ferrante, P, Ferrieri, P, Ferry, T, Feuchtinger, T, Finegold, S, Fingerle, V, Fitch, M, Fitzgerald, R, Flori, P, Fluit, A, Fontana, R, Fournier, PE, François, M, Francois, P, Freedman, DO, Friedrich, A, Gallego, L, Gallinella, G, Gangneux, J-P, Gannon, V, Garbarg-Chenon, A, Garbino, J, Garnacho-Montero, J, Gatermann, Soeren, Gautret, P, Gentile, G, Gerlich, W, Ghannoum, M, Ghebremedhin, B, Ghigo, E, Giamarellos-Bourboulis, E, Girgis, R, Giske, C, Glupczynski, Y, Gnarpe, J, Gomez-Barrena, E, Gorwitz, RJ, Gosselin, R, Goubau, P, Gould, E, Gradel, K, Gray, J, Gregson, D, Greub, G, Grijalva, CG, Groll, A, Groschup, M, Gutiérrez, J, Hackam, DG, Hall, WA, Hallett, R, Hansen, S, Harbarth, S, Harf-Monteil, C, Hasanjani, Roushan MR, Hasler, P, Hatchette, T, Hauser, P, He, Q, Hedges, A, Helbig, J, Hennequin, C, Herrmann, B, Hezode, C, Higgins, P, Hoesli, I, Hoiby, N, Hope, W, Houvinen, P, Hsu, LY, Huard, R, Humphreys, H, Icardi, M, Imoehl, M, Ivanova, K, Iwamoto, T, Izopet, J, Jackson, Y, Jacobsen, K, Jang, TN, Jasir, A, Jaulhac, B, Jaureguy, F, Jefferies, JM, Jehl, F, Johnstone, J, Joly-Guillou, M-L, Jonas, M, Jones, M, Joukhadar, C, Kahl, B, Kaier, K, Kaiser, L, Kato, H, Katragkou, A, Kearns, A, Kern, W, Kerr, K, Kessin, R, Kibbler, C, Kimberlin, D, Kittang, B, Klaassen, C, Kluytmans, J, Ko, W-C, Koh, W-J, Kostrzewa, M, Kourbeti, I, Krause, R, Krcmery, V, Krizova, P, Kuijper, E, Kullberg, B-J, Kumar, G, Kunin, CM, La Scola, B, Lagging, M, Lagrou, K, Lamagni, T, Landini, P, Landman, D, Larsen, A, Lass-Floerl, C, Laupland, K, Lavigne, JP, Leblebicioglu, H, Lee, B, Lee, CH, Leggat, P, Lehours, P, Leibovici, Lonard, Leon, L, Leonard, N, Leone, M, Lescure, X, Lesprit, P, Levy, PY, Lew, D, Lexau, CA, Li, S-Y, Li, W, Lieberman, D, Lina, B, Lina, G, Lindsay, JA, Livermore, D, Lorente, L, Lortholary, O, Lucet, J-C, Lund, B, Lütticken, R, MacLeod, C, Madhi, S, Maertens, J, Maggi, F, Maiden, M, Maillard, J-Y, Maira-Litran, T, Maltezou, H, Manian, FA, Mantadakis, E, Maragakis, L, Marcelin, A-G, Marchaim, D, Marchetti, O, Marcos, M, Markotic, A, Martina, B, Martínez, J, Martinez, J-L, Marty, F, Maurin, M, McGee, L, Mediannikov, O, Meersseman, W, Megraud, F, Meletiadis, J, Mellmann, A, Meyer, E, Meyer, W, Meylan, P, Michalopoulos, A, Micol, R, Midulla, F, Mikami, Y, Miller, RF, Miragaia, M, Miriagou, V, Mitchell, TJ, Miyakis, S, Mokrousov, I, Monecke, S, Mönkemüller, K, Monno, L, Monod, M, Morales, G, Moriarty, F, Morosini, I, Mortensen, E, Mubarak, K, Mueller, B, Mühlemann, K, Muñoz Bellido, JL, Murray, P, Muscillo, M, Mylotte, J, Naessens, A, Nagy, E, Nahm, MH, Nassif, X, Navarro, D, Navarro, F, Neofytos, D, Nes, I, Ní Eidhin, D, Nicolle, L, Niederman, MS, Nigro, G, Nimmo, G, Nordmann, P, Nougairède, A, Novais, A, Nygard, K, Oliveira, D, Orth, D, Ortiz, JR, Osherov, N, Österblad, M, Ostrosky-Zeichner, L, Pagano, L, Palamara, AT, Pallares, R, Panagopoulou, P, Pandey, P, Panepinto, J, Pappas, G, Parkins, M, Parola, P, Pasqualotto, A, Pasteran, F, Paul, M, Pawlotsky, J-M, Peeters, M, Peixe, L, Pepin, J, Peralta, G, Pereyre, S, Perfect, JR, Petinaki, E, Petric, M, Pettigrew, M, Pfaller, M, Philipp, M, Phillips, G, Pichichero, M, Pierangeli, A, Pierard, D, Pigrau, C, Pilishvili, T, Pinto, F, Pistello, M, Pitout, J, Poirel, L, Poli, G, Poppert, S, Posfay-Barbe, K, Pothier, P, Poxton, I, Poyart, C, Pozzetto, B, Pujol, M, Pulcini, C, Punyadeera, C, Ramirez, M, Ranque, S, Raoult, D, Rasigade, J-P, Re, MC, Reilly, JS, Reinert, R, Renaud, B, Rice, L, Rich, S, Richet, H, Rigouts, L, Riva, E, Rizzo, C, Robotham, J, Rodicio, MR, Rodriguez, J, Rodriguez-Bano, J, Rogier, C, Roilides, E, Rolain, J-M, Rooijakkers, S, Rooney, P, Rossi, F, Rotimi, V, Rottman, M, Roux, V, Ruhe, J, Russo, G, Sadowy, E, Sagel, U, Said, SI, Saijo, M, Sak, B, Sa-Leao, R, Sanders, EAM, Sanguinetti, M, Sarrazin, C, Savelkoul, P, Scheifele, D, Schmidt, W-P, Schønheyder, H, Schönrich, G, Schrenzel, J, Schubert, S, Schwarz, K, Schwarz, S, Sefton, A, Segondy, M, Seifert, H, Seng, P, Senneville, E, Sexton, D, Shafer, RW, Shalit, I, Shankar, N, Shata, TM, Shields, J, Sibley, C, Sicinschi, L, Siljander, T, Simitsopoulou, M, Simoons-Smit, AM, Sissoko, D, Sjögren, J, Skiada, A, Skoczynska, A, Skov, R, Slack, M, Sogaard, M, Sola, C, Soriano, A, Sotto, A, Sougakoff, W, Souli, M, Spelberg, B, Spelman, D, Spiliopoulou, I, Springer, B, Stefani, S, Stein, A, Steinbach, WJ, Steinbakk, M, Strakova, L, Strenger, V, Sturm, P, Sullivan, P, Sutton, D, Symmons, D, Tacconelli, E, Tamalet, C, Tang, JW, Tang, Y-W, Tattevin, P, Thibault, V, Thomsen, RW, Thuny, F, Tong, S, Torres, C, Townsend, R, Tristan, A, Trouillet, J-L, Tsai, H-C, Tsitsopoulos, P, Tuerlinckx, D, Tulkens, P, Tumbarello, M, Tureen, J, Turnidge, JD, Turriziani, O, Tutuian, R, Uçkay, I, Upton, M, Vabret, A, Vamvakas, EC, van den Boom, D, Van Eldere, J, van Leeuwen, W, van Strijp, J, Van Veen, S, Vandamme, P, Vandenesch, F, Vayssier, M, Velin, D, Venditti, M, Venter, M, Venuti, A, Vergnaud, G, Verheij, T, Verhofstede, C, Viscoli, C, Vizza, CD, Vogel, U, Waller, A, Wang, YF, Warn, P, Warris, A, Wauters, G, Weidmann, M, Weill, F-X, Weinberger, M, Welch, D, Wellinghausen, N, Wheat, J, Widmer, A, Wild, F, Willems, R, Willinger, B, Winstanley, C, Witte, W, Wolff, M, Wong, F, Wootton, M, Wyllie, D, Xu, W, Yamamoto, S, Yaron, S, Yildirim, I, Zaoutis, T, Zazzi, M, Zbinden, R, Zehender, Gianguglielmo G, Zemlickova, H, Zerbini, ML, Zhang, L, Zhang, Y, Zhao, Y-D, Zhu, Z, and Zimmerli, W
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- 2011
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18. The blp locus of Streptococcus pneumoniae plays a limited role in the selection of which strains can co-colonize the human nasopharynx
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Valente, C, Dawid, S, Pinto, FR, Hinds, J, Simões, AS, Gould, KA, Mendes, LA, de Lencastre, H, and Sá-Leão, R
- Abstract
Nasopharyngeal colonization is important for Streptococcus pneumoniae evolution, providing the opportunity for horizontal gene transfer when multiple strains co-occur. Although colonization with more than one strain of pneumococcus is common, the factors that influence the ability of strains to co-exist are not known. A highly variable blp (bacteriocin-like peptide) locus has been identified in all sequenced strains of S. pneumoniae This locus controls the regulation and secretion of bacteriocins, small peptides that target other bacteria. In this study, we analyzed a series of co-colonizing isolates to evaluate the impact of the blp locus on human colonization to determine whether competitive phenotypes of bacteriocin secretion restrict co-colonization.We identified a collection of 135 nasopharyngeal samples with two or more strains totaling 285 isolates. The blp locus of all strains was characterized genetically with regards to pheromone type, bacteriocin/immunity content and potential for locus functionality. Inhibitory phenotypes of bacteriocin secretion and locus activity were assessed through overlay assays. Isolates from single colonization (n=298) were characterized for comparison.Co-colonizing strains had a high diversity of blp cassettes; approximately one third displayed an inhibitory phenotype in vitro Despite in vitro evidence of competition, pneumococci co-colonized individuals independently of their blp pheromone type (p=0.577), bacteriocin/immunity content, blp locus activity (p=0.798) and inhibitory phenotype (p=0.716). In addition, no significant differences were observed when single and co-colonizing strains were compared.Despite clear evidence of blp-mediated competition in experimental models, our study suggests that the blp locus plays a limited role in restricting pneumococcal co-colonization in humans. IMPORTANCE: Nasopharyngeal colonization with Streptococcus pneumoniae (pneumococcus) is important for pneumococcal evolution as it represents the major site for horizontal gene transfer when multiple strains co-occur, a phenomenon known as co-colonization. Understanding how pneumococcal strains interact within the competitive environment of the nasopharynx is of chief importance in the context of pneumococcal ecology. In this study we used an unbiased collection of naturally co-occurring pneumococcal strains and showed that a biological process frequently used by bacteria for competition - bacteriocin production - is not decisive in the co-existence of pneumococci in the host, contrary to what has been shown in experimental models.
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- 2016
19. Ability of Antibiotic-Resistant Nonvaccine-Type Pneumococcal Clones to Cause Otitis Media in an Infant Mouse Model of Pneumococcal-Influenza Virus Coinfection
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Frazão, N., Hermans, P.W.M., Selm, S. van, Sá-Leão, R., Lencastre, H. de, Tomasz, A., Diavatopoulos, D.A., Frazão, N., Hermans, P.W.M., Selm, S. van, Sá-Leão, R., Lencastre, H. de, Tomasz, A., and Diavatopoulos, D.A.
- Abstract
Item does not contain fulltext
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- 2016
20. Related citations Select item 233693894. Overview of molecular typing methods for outbreak detection and epidemiological surveillance
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Sabat, A.J., Budimir, Ana, Nashev, D., Sá-Leão, R., van Dijl, J., Laurent, F., Grundmann, H., and Friedrich, A.W.
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molecular typing methods ,outbreak ,detection ,epidemiological surveillance - Abstract
Typing methods for discriminating different bacterial isolates of the same species are essential epidemiological tools in infection prevention and control. Traditional typing systems based on phenotypes, such as serotype, biotype, phage-type, or antibiogram, have been used for many years. However, more recent methods that examine the relatedness of isolates at a molecular level have revolutionised our ability to differentiate among bacterial types and subtypes. Importantly, the development of molecular methods has provided new tools for enhanced surveillance and outbreak detection. This has resulted in better implementation of rational infection control programmes and efficient allocation of resources across Europe. The emergence of benchtop sequencers using next generation sequencing technology makes bacterial whole genome sequencing (WGS) feasible even in small research and clinical laboratories. WGS has already been used for the characterisation of bacterial isolates in several large outbreaks in Europe and, in the near future, is likely to replace currently used typing methodologies due to its ultimate resolution. However, WGS is still too laborious and time-consuming to obtain useful data in routine surveillance. Also, a largely unresolved question is how genome sequences must be examined for epidemiological characterisation. In the coming years, the lessons learnt from currently used molecular methods will allow us to condense the WGS data into epidemiologically useful information. On this basis, we have reviewed current and new molecular typing methods for outbreak detection and epidemiological surveillance of bacterial pathogens in clinical practice, aiming to give an overview of their specific advantages and disadvantages.
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- 2013
21. Differences in genotype and virulence among four multidrug-resistant Streptococcus pneumoniae isolates belonging to the PMEN1 clone
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Tse, H., Hiller, N.L., Eutsey, R.A., Powell, E., Earl, J.P., Janto, B., Martin, D.P., Dawid, S., Ahmed, A., Longwell, M.J., Dahlgren, M.E., Ezzo, S., Tettelin, H., Daugherty, S.C., Mitchell, T.J., Hillman, T.A., Buchinsky, F.J., Tomasz, A., de Lencastre, H., Sá-Leão, R., Post, J.C., Hu, F.Z., and Ehrlich, G.D.
- Abstract
We report on the comparative genomics and characterization of the virulence phenotypes of four S. pneumoniae strains that belong to the multidrug resistant clone PMEN1 (Spain23F ST81). Strains SV35-T23 and SV36-T3 were recovered in 1996 from the nasopharynx of patients at an AIDS hospice in New York. Strain SV36-T3 expressed capsule type 3 which is unusual for this clone and represents the product of an in vivo capsular switch event. A third PMEN1 isolate - PN4595-T23 - was recovered in 1996 from the nasopharynx of a child attending day care in Portugal, and a fourth strain - ATCC700669 - was originally isolated from a patient with pneumococcal disease in Spain in 1984. We compared the genomes among four PMEN1 strains and 47 previously sequenced pneumococcal isolates for gene possession differences and allelic variations within core genes. In contrast to the 47 strains - representing a variety of clonal types - the four PMEN1 strains grouped closely together, demonstrating high genomic conservation within this lineage relative to the rest of the species. In the four PMEN1 strains allelic and gene possession differences were clustered into 18 genomic regions including the capsule, the blp bacteriocins, erythromycin resistance, the MM1-2008 prophage and multiple cell wall anchored proteins. In spite of their genomic similarity, the high resolution chinchilla model was able to detect variations in virulence properties of the PMEN1 strains highlighting how small genic or allelic variation can lead to significant changes in pathogenicity and making this set of strains ideal for the identification of novel virulence determinants
- Published
- 2011
22. Molecular typing of methicillin-resistant Staphylococcus aureus by pulsed-field gel electrophoresis: Comparison of results obtained in a multilaboratory effort using identical protocols and MRSA strains
- Author
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Chung, M. De Lencastre, H. Matthews, P. Tomasz, A. Adamsson, I. Aires de Sousa, M. Camou, T. Cocuzza, C. Corso, A. Couto, I. Dominguez, A. Gniadkowski, M. Goering, R. Gomes, A. Kikuchi, K. Marchese, A. Mato, R. Melter, O. Oliveira, D. Sá-Leão, R. Santos Sanches, I. Santos Sanches, I. Tassios, P.T. Villari, P. Multilaboratory Project Collaborators
- Abstract
Pulsed-field gel electrophoresis (PFGE) has become the gold standard of molecular methods in epidemiological investigations. In spite of its high resolving power, use of the method has been hampered by inadequate laboratory-to-laboratory reproducibility. In the project described here we have addressed this problem by organizing a multilaboratory effort in which the same bacterial strains (subtype variants of the Iberian and Brazilian methicillin-resistant Staphylococcus aureus-MRSA-clones) were analyzed by twenty Investigators in thirteen different laboratories according to an indentical protocol, which is reproduced here in detail. PFGE patterns obtained were analyzed at a central laboratory in order to identify specific technical problems that produced substandard macrorestriction patterns. The results including the specific technical problems and their most likely causes are described in this communication. Also listed are seven major epidemic clones of MRSA which have been characterized by molecular fingerprinting techniques and the prototypes of which have been deposited at the American Type Culture Collection, from where they will be available for interested investigators for the purpose of typing MRSA isolates. It is hoped that this communication will contribute to the improvement of the reproducibility and technical/aesthetic quality of PFGE analysis.
- Published
- 2009
23. Selection of Distinctive Colony Morphologies for Detection of Multiple Carriage of Streptococcus pneumoniae
- Author
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de Lencastre H, Sá-Leão R, and Valente C
- Subjects
Microbiology (medical) ,Bacteriological Techniques ,Coinfection ,business.industry ,Carrier state ,medicine.disease ,medicine.disease_cause ,Pneumococcal Infections ,Microbiology ,Pneumococcal infections ,Streptococcus pneumoniae ,Infectious Diseases ,Carriage ,Child, Preschool ,Carrier State ,Pediatrics, Perinatology and Child Health ,Humans ,Medicine ,Child ,business ,Selection (genetic algorithm) - Published
- 2013
24. Prevalence, risk factors, and epidemiology of methicillin-resistantStaphylococcus aureus carried by adults over 60 years of age
- Author
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Almeida, S. T., primary, Nunes, S., additional, Paulo, A. C. S., additional, Faria, N. A., additional, de Lencastre, H., additional, and Sá-Leão, R., additional
- Published
- 2014
- Full Text
- View/download PDF
25. Molecular typing of methicillin-resistant Staphylococcus aureus by pulsed-field gel electrophoresis: Comparison of results obtained in a multilaboratory effort using identical protocols and MRSA strains
- Author
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Chung, M, de Lencastre, H, Matthews, P, Tomasz, A, Adamsson, I, Aires de Sousa, M, Camou, T, Cocuzza, C, Corso, A, Couto, I, Dominguez, A, Gniadkowski, M, Goering, R, Gomes, A, Kikuchi, K, Marchese, A, Mato, R, Melter, O, Oliveira, D, Palacio, R, Sá Leão, R, Santos Sanches, I, Song, J, Tassios, P, Villari, P, COCUZZA, CLEMENTINA ELVEZIA, Song, JH, Tassios, PT, Villari, P., Chung, M, de Lencastre, H, Matthews, P, Tomasz, A, Adamsson, I, Aires de Sousa, M, Camou, T, Cocuzza, C, Corso, A, Couto, I, Dominguez, A, Gniadkowski, M, Goering, R, Gomes, A, Kikuchi, K, Marchese, A, Mato, R, Melter, O, Oliveira, D, Palacio, R, Sá Leão, R, Santos Sanches, I, Song, J, Tassios, P, Villari, P, COCUZZA, CLEMENTINA ELVEZIA, Song, JH, Tassios, PT, and Villari, P.
- Abstract
Pulsed-field gel electrophoresis (PFGE) has become the gold standard of molecular methods in epidemiological investigations. In spite of its high resolving power, use of the method has been hampered by inadequate laboratory-to-laboratory reproducibility. In the project described here we have addressed this problem by organizing a multilaboratory effort in which the same bacterial strains (subtype variants of the Iberian and Brazilian methicillin-resistant Staphylococcus aureus--MRSA--clones) were analyzed by twenty investigators in thirteen different laboratories according to an indentical protocol, which is reproduced here in detail. PFGE patterns obtained were analyzed at a central laboratory in order to identify specific technical problems that produced substandard macrorestriction patterns. The results including the specific technical problems and their most likely causes are described in this communication. Also listed are seven major epidemic clones of MRSA which have been characterized by molecular fingerprinting techniques and the prototypes of which have been deposited at the American Type Culture Collection, from where they will be available for interested investigators for the purpose of typing MRSA isolates. It is hoped that this communication will contribute to the improvement of the reproducibility and technical/aesthetic quality of PFGE analysis.
- Published
- 2009
26. S46 Invasive disease potential of pneumococcal clones carried by children
- Author
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de Lencastre, H., primary, Sá-Leão, R., additional, Ramirez, M., additional, and Melo-Cristino, J., additional
- Published
- 2007
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- View/download PDF
27. Prevalence, risk factors, and epidemiology of methicillin-resistant Staphylococcus aureus carried by adults over 60 years of age.
- Author
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Almeida, S., Nunes, S., Paulo, A., Faria, N., Lencastre, H., and Sá-Leão, R.
- Subjects
EPIDEMIOLOGY ,METHICILLIN-resistant staphylococcus aureus ,LOGISTIC regression analysis ,CONFIDENCE intervals ,MULTIDRUG resistance ,DISEASE risk factors - Abstract
The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in the community in Portugal is not completely understood. To evaluate S. aureus and MRSA carriage among the elderly, we conducted a large cross-sectional study between April 2010 and December 2012. A total of 3,361 adults over 60 years of age were screened for S. aureus nasopharyngeal and oropharyngeal carriage. MRSA were characterized by staphylococcal cassette chromosome mec (SCC mec) typing, spa typing, multilocus sequence typing (MLST), and tested for the presence of Panton-Valentine leukocidin (PVL). Risk factors for MRSA carriage were identified by multiple logistic regression analysis. The prevalence of S. aureus and MRSA carriage among the elderly was 20.1 % and 1.8 %, respectively. The risk of being an MRSA carrier was higher among the elderly living in retirement homes [odds ratio (OR) = 2.90, 95 % confidence interval (CI): 1.48-5.48] and those that had been hospitalized in the previous year (OR = 2.64, 95 % CI: 1.47-4.58). Among the 62 MRSA isolates, 64.5 % were multidrug-resistant and none carried PVL. Most MRSA (82.3 %) were related to three hospital-associated (HA-MRSA) clones disseminated in Portugal: ST105-II (New York/Japan clone; 43.5 %), ST5-IVc (Pediatric clone; 19.4 %), and ST22-IVh (EMRSA-15 clone; 19.4 %). The New York/Japan and Pediatric clones were significantly associated with carriers living in retirement homes, while the EMRSA-15 clone was associated with carriers that had been hospitalized. We conclude that the elderly population in Portugal is essentially free of MRSA. Given the current European societal challenges for a healthy active aging, these results are of importance to healthcare professionals and public authorities to decide on strategies to promote health in this age group. [ABSTRACT FROM AUTHOR]
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- 2015
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28. Trends in Drug Resistance, Serotypes, and Molecular Types of Streptococcus pneumoniae Colonizing Preschool-Age Children Attending Day Care Centers in Lisbon, Portugal: a Summary of 4 Years of Annual Surveillance
- Author
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Nunes, S., primary, Sá-Leão, R., additional, Carriço, J., additional, Alves, C. R., additional, Mato, R., additional, Avô, A. Brito, additional, Saldanha, J., additional, Almeida, J. S., additional, Sanches, I. Santos, additional, and de Lencastre, H., additional
- Published
- 2005
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29. Clonal and Antibiotic Resistance Profiles of Methicillin-ResistantStaphylococcus aureus(MRSA) from a Portuguese Hospital over Time
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Amorim, M.L., primary, Aires de Sousa, M., additional, Sanches, I. Santos, additional, Sá-Leão, R., additional, Cabeda, J.M., additional, Amorim, J.M., additional, and de Lencastre, H., additional
- Published
- 2002
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30. Overview of molecular typing methods for outbreak detection and epidemiological surveillance.
- Author
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Sabat, A. J., Budimir, A., Nashev, D., Sá-Leão, R., van Dijl, J. M., Laurent, F., Grundmann, H., and Friedrich, A. W.
- Published
- 2013
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31. Carriage of internationally spread clones of Streptococcus pneumoniae with unusual drug resistance patterns in children attending day care centers in Lisbon, Portugal [corrected] [published erratum appears in J INFECT DIS 2000; 182: 1581].
- Author
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Sá-Leão R, Tomasz A, Sanches IS, Brito-Avô A, Vilhelmsson SE, Kristinsson KG, and de Lencastre H
- Abstract
Over half (259/503) of drug-resistant (DR) pneumococci colonizing healthy children attending day care centers in Lisbon were identified by molecular typing methods as representatives of several internationally spread clones. These included the 2 penicillin-resistant pandemic Spanish/USA and French/Spanish clones (21% of all DR pneumococci) and 5 new lineages with unusual antibiotypes (accounting for an additional 30% of all DR pneumococci). The most characteristic feature of the latter group was the high frequency of resistance to macrolides and tetracycline and very low or no resistance to penicillin. These observations provide support for the notion that the nasopharyngeal flora of children in day care centers may be a global reservoir of worldwide prevalent strains of DR pneumococci. Copyright © 2000 The University of Chicago [ABSTRACT FROM AUTHOR]
- Published
- 2000
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32. Clonal and Antibiotic Resistance Profiles of Methicillin-Resistant Staphylococcus aureus (MRSA) from a Portuguese Hospital over Time
- Author
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Amorim, M.L., Aires de Sousa, M., Sanches, I. Santos, Sá-Leão, R., Cabeda, J.M., Amorim, J.M., and de Lencastre, H.
- Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered from a general hospital in Oporto, Portugal, during two periods (1992-1993 and 1996-2000) were characterized by pulsed-field gel electrophoresis (PFGE) of SmaI fragments, and by hybridization of ClaI digests with mecA and Tn554 probes, discriminating the isolates in mecA::Tn554::PFGE genotypes. In addition, a representative sample of the defined genotypes was characterized by multilocus sequence typing (MLST) and SCCmec (staphylococcal cassette chromosome mec) typing, generating the corresponding ST-SCCmec types. In 1992-1993, 77% of MRSA belonged to the Iberian clone (genotype I::E::A or ST247-IA). In 1996-2000, the frequency of this clone decreased to 19% and the majority (69%) of the isolates belonged to another international clone, the Brazilian MRSA (genotype XI::B::B or ST239-IIIA). Trimethoprim/sulfamethoxazole (SXT) was confirmed to be an important phenotypic marker to distinguish the Iberian (SXT-susceptible) and the Brazilian (SXT-resistant) clones in MRSA isolates from Portugal. Our observations document major shifts in the dominant MRSA clonal types that occurred in this hospital since 1992, suggesting a selective advantage of the Brazilian relatively to the Iberian clone. In addition to these two MRSA clones that are the most frequent in Portuguese hospitals since the early 1990s, sporadic MRSA clones (representing 14% of the total) were identified and characterized.
- Published
- 2002
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33. Genetic diversity and clonal patterns among antibiotic-susceptible and -resistant streptococcus pneumoniae colonizing children: Day care centers as autonomous epidemiological units
- Author
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Sá-Leão, R., Alexander Tomasz, Sanches, S. I., Nunes, S., Alves, C. R., Avô, A. B., Saldanha, J., Kristinsson, K. G., and Lencastre, H.
34. Low prevalence of methicillin-resistant strains among Staphylococcus aureus colonizing young and healthy members of the community in Portugal
- Author
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Sá-Leão, R., Sanches, I. S., Isabel Couto, Alves, C. R., and Lencastre, H.
35. Carriage of respiratory tract pathogens and molecular epidemiology of Streptococcus pneumoniae colonization in healthy children attending day care centers in Lisbon, Portugal
- Author
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Lencastre, H., Kristinsson, K. G., Brito-Avô, A., Sanches, I. S., Sá-Leão, R., Saldanha, J., Sigvaldadottir, E., Karlsson, S., Duarte Oliveira, Mato, R., Aires Sousa, M., and Tomasz, A.
36. Molecular typing of methicillin-resistant Staphylococcus aureus by pulsed-field gel electrophoresis: comparison of results obtained in a multilaboratory effort using identical protocols and MRSA strains
- Author
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Duarte C. Oliveira, Panayotis T. Tassios, Richard V. Goering, Ken Kikuchi, Marilyn Chung, Jae-Hoon Song, Anna Marchese, R. Mato, Raquel Sá-Leão, Alejandra Corso, Marek Gniadkowski, Oto Melter, Rosario Palacio, Peter Matthews, Paolo Villari, Angeles Dominguez, Teresa Camou, Marta Aires de Sousa, Hermínia de Lencastre, Isabel Couto, Clementina Cocuzza, Ana Sara Gomes, Ilda Santos Sanches, Alexander Tomasz, Chung, M, de Lencastre, H, Matthews, P, Tomasz, A, Adamsson, I, Aires de Sousa, M, Camou, T, Cocuzza, C, Corso, A, Couto, I, Dominguez, A, Gniadkowski, M, Goering, R, Gomes, A, Kikuchi, K, Marchese, A, Mato, R, Melter, O, Oliveira, D, Palacio, R, Sá Leão, R, Santos Sanches, I, Song, J, Tassios, P, and Villari, P
- Subjects
Microbiology (medical) ,Staphylococcus aureus ,Meticillin ,Immunology ,Biology ,medicine.disease_cause ,Microbiology ,Central laboratory ,Molecular typing ,Bacterial Typing Technique ,medicine ,Pulsed-field gel electrophoresis ,Humans ,Typing ,Pharmacology ,Pulsed-Field Gel Electrophoresis (PFGE) ,Reproducibility of Results ,Reference Standards ,Staphylococcal Infections ,Methicillin-resistant Staphylococcus aureus ,Bacterial Typing Techniques ,Electrophoresis, Gel, Pulsed-Field ,MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA ,Staphylococcus aureu ,Methicillin Resistance ,Molecular Fingerprinting ,Pfge analysis ,Laboratories ,medicine.drug - Abstract
Pulsed-field gel electrophoresis (PFGE) has become the gold standard of molecular methods in epidemiological investigations. In spite of its high resolving power, use of the method has been hampered by inadequate laboratory-to-laboratory reproducibility. In the project described here we have addressed this problem by organizing a multilaboratory effort in which the same bacterial strains (subtype variants of the Iberian and Brazilian methicillin-resistant Staphylococcus aureus--MRSA--clones) were analyzed by twenty investigators in thirteen different laboratories according to an indentical protocol, which is reproduced here in detail. PFGE patterns obtained were analyzed at a central laboratory in order to identify specific technical problems that produced substandard macrorestriction patterns. The results including the specific technical problems and their most likely causes are described in this communication. Also listed are seven major epidemic clones of MRSA which have been characterized by molecular fingerprinting techniques and the prototypes of which have been deposited at the American Type Culture Collection, from where they will be available for interested investigators for the purpose of typing MRSA isolates. It is hoped that this communication will contribute to the improvement of the reproducibility and technical/aesthetic quality of PFGE analysis.
- Published
- 2000
37. Streptococcus pneumoniae carriage, serotypes, genotypes, and antimicrobial resistance trends among children in Portugal, after introduction of PCV13 in National Immunization Program: A cross-sectional study.
- Author
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Candeias C, Almeida ST, Paulo AC, Simões AS, Ferreira B, Cruz AR, Queirós M, Touret T, Brito-Avô A, de Lencastre H, and Sá-Leão R
- Subjects
- Humans, Cross-Sectional Studies, Portugal epidemiology, Child, Preschool, Female, Male, Infant, Child, Anti-Bacterial Agents pharmacology, Drug Resistance, Bacterial, Prevalence, Vaccines, Conjugate immunology, Vaccines, Conjugate administration & dosage, Microbial Sensitivity Tests, Streptococcus pneumoniae drug effects, Streptococcus pneumoniae classification, Streptococcus pneumoniae genetics, Streptococcus pneumoniae immunology, Pneumococcal Vaccines immunology, Pneumococcal Vaccines administration & dosage, Pneumococcal Infections prevention & control, Pneumococcal Infections epidemiology, Pneumococcal Infections microbiology, Serogroup, Carrier State epidemiology, Carrier State microbiology, Immunization Programs, Genotype, Nasopharynx microbiology
- Abstract
Streptococcus pneumoniae carriage studies are crucial to monitor changes induced by use of pneumococcal conjugate vaccines and inform vaccination policies. In this cross-sectional study, we examined changes within the pneumococcal population following introduction of PCV13 in 2015 in the National Immunization Program (NIP), in Portugal. In 2018-2020 (NIP-PCV13), we obtained 1450 nasopharyngeal samples from children ≤6 years attending day-care. We assessed serotypes, antimicrobial resistance, and genotypes (MLST and GPSC) and compared findings with earlier periods: 2009-2010 (pre-PCV13), 2011-2012 (early-PCV13), and 2015-2016 (late-PCV13). Pneumococcal carriage prevalence remained stable at 60.2 %. Carriage of PCV13 serotypes was 10.7 %, markedly reduced compared to pre-PCV13 period (47.6 %). The most prevalent PCV13 serotypes were 19F, 3, and 19A all showing a significant decreasing trend compared to the pre-PCV13 period (from 7.1 % to 4.7 %, 10.1 % to 1.8 %, and 14.1 % to 1.8 %, respectively), a notable observation given the described limited effectiveness of PCV13 against serotype 3. Non-vaccinated children and children aged 4-6 years were more likely to carry PCV13 serotypes (2.5-fold, 95 %CI [1.1-5.6], and 2.9-fold, 95 %CI [1.3-6.8], respectively). The most prevalent non-PCV13 serotypes were 15B/C, 11A, 23B, 23A, and NT, collectively accounting for 51.9 % of all isolates. In total, 30.5 % of all pneumococci were potentially covered by PCV20. Resistance to penicillin (low-level) and macrolides increased significantly, from 9.3 % and 13.4 %, respectively, in the late-PCV13 period, to approximately 20 % each, mostly due to lineages expressing non-PCV13 serotypes, nearing pre-PCV13 levels. An expansion of lineages traditionally associated with PCV13 serotypes, like CC156-GPSC6 (serotype 14) and CC193-GPSC11 (serotype 19F), but now predominantly expressing non-PCV13 serotypes (11A, 15B/C, and 24F for GPSC6; and 15A and 21 for GPSC11) was noted. These findings indicate that the pneumococcal population is adapting to the pressures conferred by PCV13 and antimicrobial use and indicate the need to maintain close surveillance., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: RSL has received consulting and speaking fees from Pfizer and Merck Sharp & Dome. RSL has received funds for unrestricted research grants from Pfizer and Merck Sharp & Dome, paid directly to her institution. ABA has received consulting and speaking fees from Pfizer and Merck Sharp & Dome. All other authors declare they have no conflicts of interest., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2024
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38. A one-step low-cost molecular test for SARS-CoV-2 detection suitable for community testing using minimally processed saliva.
- Author
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da Silva SM, Amaral C, Malta-Luís C, Grilo D, Duarte AG, Morais I, Afonso G, Faria N, Antunes W, Gomes I, Sá-Leão R, Miragaia M, Serrano M, and Pimentel C
- Abstract
The gold standard for coronavirus disease 2019 diagnostic testing relies on RNA extraction from naso/oropharyngeal swab followed by amplification through reverse transcription-polymerase chain reaction (RT-PCR) with fluorogenic probes. While the test is extremely sensitive and specific, its high cost and the potential discomfort associated with specimen collection made it suboptimal for public health screening purposes. In this study, we developed an equally reliable, but cheaper and less invasive alternative test based on a one-step RT-PCR with the DNA-intercalating dye SYBR Green, which enables the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly from saliva samples or RNA isolated from nasopharyngeal (NP) swabs. Importantly, we found that this type of testing can be fine-tuned to discriminate SARS-CoV-2 variants of concern. The saliva RT-PCR SYBR Green test was successfully used in a mass-screening initiative targeting nearly 4500 asymptomatic children under the age of 12. Testing was performed at a reasonable cost, and in some cases, the saliva test outperformed NP rapid antigen tests in identifying infected children. Whole genome sequencing revealed that the antigen testing failure could not be attributed to a specific lineage of SARS-CoV-2. Overall, this work strongly supports the view that RT-PCR saliva tests based on DNA-intercalating dyes represent a powerful strategy for community screening of SARS-CoV-2. The tests can be easily applied to other infectious agents and, therefore, constitute a powerful resource for an effective response to future pandemics., (© The Author(s) 2024. Published by Oxford University Press.)
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- 2024
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39. Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae .
- Author
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Henares D, Lo SW, Perez-Argüello A, Redin A, Ciruela P, Garcia-Garcia JJ, Brotons P, Yuste J, Sá-Leão R, and Muñoz-Almagro C
- Subjects
- Humans, Child, Serotyping methods, Serogroup, Whole Genome Sequencing methods, Computational Biology, Streptococcus pneumoniae genetics, Pneumococcal Infections epidemiology
- Abstract
Whole genome sequencing (WGS)-based approaches for pneumococcal capsular typing have become an alternative to serological methods. In silico serotyping from WGS has not yet been applied to long-read sequences produced by third-generation technologies. The objective of the study was to determine the capsular types of pneumococci causing invasive disease in Catalonia (Spain) using serological typing and WGS and to compare the performance of different bioinformatics pipelines using short- and long-read data from WGS. All invasive pneumococcal pediatric isolates collected in Hospital Sant Joan de Déu (Barcelona) from 2013 to 2019 were included. Isolates were assigned a capsular type by serological testing based on anticapsular antisera and by different WGS-based pipelines: Illumina sequencing followed by serotyping with PneumoCaT, SeroBA, and Pathogenwatch vs MinION-ONT sequencing coupled with serotyping by Pathogenwatch from pneumococcal assembled genomes. A total of 119 out of 121 pneumococcal isolates were available for sequencing. Twenty-nine different serotypes were identified by serological typing, with 24F ( n = 17; 14.3%), 14 ( n = 10; 8.4%), and 15B/C ( n = 8; 6.7%) being the most common serotypes. WGS-based pipelines showed initial concordance with serological typing (>91% of accuracy). The main discrepant results were found at the serotype level within a serogroup: 6A/B, 6C/D, 9A/V, 11A/D, and 18B/C. Only one discrepancy at the serogroup level was observed: serotype 29 by serological testing and serotype 35B/D by all WGS-based pipelines. Thus, bioinformatics WGS-based pipelines, including those using third-generation sequencing, are useful for pneumococcal capsular assignment. Possible discrepancies between serological typing and WGS-based approaches should be considered in pneumococcal capsular-type surveillance studies., Competing Interests: C.M.A. reports a research grant from Pfizer laboratories paid to Sant Joan de Déu foundation and related with the submitted work, as well as fees as speaker at conferences from MSD, Pfizer and Sanofi-Pasteur. J.Y. reports research grants from Pfizer and MSD unrelated to the submitted work, as well as participation in scientific advisory boards organized by Pfizer and MSD.
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- 2023
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40. The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children.
- Author
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Paulo AC, Lança J, Almeida ST, Hilty M, and Sá-Leão R
- Subjects
- Adult, Child, Humans, Streptococcus pneumoniae genetics, Smoking, Nose, Metagenome, Firmicutes, Microbiota, Bacillus
- Abstract
Background: The microbiota of the upper respiratory tract is increasingly recognized as a gatekeeper of respiratory health. Despite this, the microbiota of healthy adults remains understudied. To address this gap, we investigated the composition of the nasopharyngeal and oropharyngeal microbiota of healthy adults, focusing on the effect of Streptococcus pneumoniae carriage, smoking habits, and contact with children., Results: Differential abundance analysis indicated that the microbiota of the oropharynx was significantly different from that of the nasopharynx (P < 0.001) and highly discriminated by a balance between the classes Negativicutes and Bacilli (AUC of 0.979). Moreover, the oropharynx was associated with a more homogeneous microbiota across individuals, with just two vs. five clusters identified in the nasopharynx. We observed a shift in the nasopharyngeal microbiota of carriers vs. noncarriers with an increased relative abundance of Streptococcus, which summed up to 30% vs. 10% in noncarriers and was not mirrored in the oropharynx. The oropharyngeal microbiota of smokers had a lower diversity than the microbiota of nonsmokers, while no differences were observed in the nasopharyngeal microbiota. In particular, the microbiota of smokers, compared with nonsmokers, was enriched (on average 16-fold) in potential pathogenic taxa involved in periodontal diseases of the genera Bacillus and Burkholderia previously identified in metagenomic studies of cigarettes. The microbiota of adults with contact with children resembled the microbiota of children. Specifically, the nasopharyngeal microbiota of these adults had, on average, an eightfold increase in relative abundance in Streptococcus sp., Moraxella catarrhalis, and Haemophilus influenzae, pathobionts known to colonize the children's upper respiratory tract, and a fourfold decrease in Staphylococcus aureus and Staphylococcus lugdunensis., Conclusions: Our study showed that, in adults, the presence of S. pneumoniae in the nasopharynx is associated with a shift in the microbiota and dominance of the Streptococcus genus. Furthermore, we observed that smoking habits are associated with an increase in bacterial genera commonly linked to periodontal diseases. Interestingly, our research also revealed that adults who have regular contact with children have a microbiota enriched in pathobionts frequently carried by children. These findings collectively contribute to a deeper understanding of how various factors influence the upper respiratory tract microbiota in adults. Video Abstract., (© 2023. BioMed Central Ltd., part of Springer Nature.)
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- 2023
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41. Clonal Changes in the Pneumococcal Population Carried by Portuguese Children during Six Years of Private Use of the 13-Valent Pneumococcal Conjugate Vaccine: the Relative Contribution of Clonal Expansion, Clonal Emergence, and Capsular Switch Events.
- Author
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Candeias C, Félix S, Handem S, de Lencastre H, and Sá-Leão R
- Abstract
In Portugal, the 13-valent pneumococcal conjugate vaccine (PCV13) was available for private use from 2010 to 2015 and it was introduced in the National Immunization Program in 2015. We have reported that private use of PCV13 led to extensive serotype replacement and an increase in antimicrobial susceptibility among pneumococci carried by healthy children. We investigated which clonal changes concurred with these observations. A total of 657 pneumococcal strains, representative of a collection of 2,615 isolates, were genotyped by multilocus sequence typing (MLST). The isolates were recovered in 2009 to 2010 (pre-PCV13), 2011 to 2012 (early PCV13), and 2015 to 2016 (late PCV13) from children attending day care centers in two regions of Portugal (one urban, one rural). One-hundred seventy-one sequence types (STs) were identified, corresponding to 18 clonal complexes (CCs) and 58 singletons. Most CCs ( n = 17) and several singletons ( n = 16) were found in both regions, indicating that they were geographically disseminated. Clonal complexes expressing PCV13 serotypes in circulation in the late PCV13 period were a subset of the ones identified in the pre-PCV13 period and were often associated with antimicrobial resistance. Among those, the most frequent in both regions was CC179, a multidrug-resistant clone of serotype 19F. Serotype replacement, following PCV13 use, was mainly due to expansion of the susceptible lineages expressing non-PCV13 serotypes already in circulation in the pre-PCV13 period. The emergence of ST53, associated with serotype 8, a major cause of disease in several European countries, was observed in the rural region. Potential capsular switching events, unrelated to PCV13 use, were detected. This study improves our understanding of changes triggered by the private use of PCV13 in Portugal. IMPORTANCE Streptococcus pneumoniae (pneumococcus) is a major human respiratory pathogen linked with high morbidity, mortality, and health care-associated costs worldwide. This bacterium often colonizes asymptomatically healthy children. Colonization is a prerequisite for disease and is also essential for transmission between individuals. The 13-valent pneumococcal conjugate vaccine targets 13 of 101 capsular types of pneumococci described to date. This vaccine not only prevents pneumococcal disease but also impacts colonization by decreasing the carriage of vaccine serotypes. Consequently, serotype replacement occurs. The clonal changes occurring during serotype replacement may be due to various mechanisms, such as clonal expansion, emergence, extinction, or capsular switch (vaccine escape). This study shows that in Portugal, the use of PCV13 has led to significant changes in clonal composition and that these were mainly due to the clonal expansion of lineages expressing serotypes not included in the vaccine.
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- 2023
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42. Streptococcus pneumoniae carriage studies in adults: Importance, challenges, and key issues to consider when using quantitative PCR-based approaches.
- Author
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Miellet WR, Almeida ST, Trzciński K, and Sá-Leão R
- Abstract
Streptococcus pneumoniae causes significant morbidity and mortality among older adults. Detection of pneumococcal carriage is an accepted endpoint in pneumococcal conjugate vaccine studies. However, low sensitivity of culture-based approaches and nasopharyngeal samples have hampered adult S. pneumoniae carriage studies in the past. In contrast, detection of adult S. pneumoniae carriers with qPCR-based approaches can achieve high sensitivity and specificity and qPCR-based testing of oral samples improves accuracy of adult carriage detection. In this Viewpoint we outline a strategy for accurate qPCR-based testing. We recommend a dual-target approach for S. pneumoniae qPCR detection as no genetic target is universally present among or solely unique to it. Furthermore, we advise the evaluation of concordance among quantified qPCR targets to improve the accuracy of S. pneumoniae testing and qPCR-based serotyping. We do not recommend omission of qPCR-based oral sample testing as it will likely result in an underestimation of true adult carrier rates., Competing Interests: KT reports receiving consultation and speaking fees and funds for unrestricted research grants from Pfizer, and funds for unrestricted research grants and consultation fees from Merck Sharp & Dohme, all paid directly to his home institution and none related to the present work. RS-L reports receiving consultation and speaking fees from Pfizer and consulting fees from Merck (US). RS-L reports also receiving funds for unrestricted research grants from Pfizer and Merck Sharp & Dohme not related to the present work, paid directly to her home institution. The remaining authors 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., (Copyright © 2023 Miellet, Almeida, Trzciński and Sá-Leão.)
- Published
- 2023
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43. Haemophilus influenzae Carriage among Healthy Children in Portugal, 2015-2019.
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Bajanca-Lavado MP, Cavaco L, Fernandes M, Touret T, Candeias C, Simões AS, and Sá-Leão R
- Abstract
Haemophilus influenzae is an important cause of mucosal and invasive infections and a common colonizer of the upper respiratory tract. As there are no recent data on H. influenzae carriage in Portugal, we aimed to characterize carriage samples and investigate possible parallelisms with disease isolates. Between 2016-2019, 1524 nasopharyngeal samples were obtained from children (0-6 years) attending day-care. H. influenzae were serotyped and screened for β-lactamase production. Strains producing β-lactamase and/or those that were encapsulated were further characterized by antibiotype; encapsulated strains were also investigated for MLST and the presence of antimicrobial resistance and virulence genes (extracted from whole genome sequencing). The overall carriage rate was 84.1%. Most isolates (96.7%) were nonencapsulated. Encapsulated strains were of serotypes f (1.8%), e (1.1%), a (0.3%), and b (0.1%). MLST showed clonality within serotypes. Although the lineages were the same as those that were described among disease isolates, colonization isolates had fewer virulence determinants. Overall, 7.5% of the isolates were β-lactamase positive; one isolate had bla
TEM-82 , which has not been previously described in H. influenzae . A single isolate, which was identified as H. parainfluenzae , had an incomplete f-like cap locus. In conclusion, circulation of serotype b is residual. The few encapsulated strains are genetically related to disease-causing isolates. Thus, surveillance of H. influenzae carriage should be maintained.- Published
- 2022
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44. World Health Organization (WHO) Standard Methods for Pneumococcal Carriage Studies.
- Author
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Turner P, Sá-Leão R, Greenhill A, Leach A, and Satzke C
- Subjects
- Carrier State epidemiology, Humans, Infant, Nasopharynx, Pneumococcal Vaccines, World Health Organization, Pneumococcal Infections epidemiology, Pneumococcal Infections prevention & control, Streptococcus pneumoniae
- Abstract
Competing Interests: Potential conflicts of interest. A. L. reports MSD contract for pneumococcal carriage data analysis, funds paid to institution, outside of the submitted work. R. S.-L. reports funds directly paid to institution from Pfizer as investigator initiated research grant outside of the submitted work and received payment for lectures paid directly to self from Pfizer. C. S. reports being lead investigator on a Merck Investigator Studies Program grant funded by MSD on pneumococcal serotype epidemiology in children with empyema paid to institution and investigator on a clinical research collaboration on PVC vaccination in Mongolia from Pfizer paid to the institution, both outside of the submitted work. P. T. reports PI of the ACORN AMR surveillance project (grant number 222156/Z/20/Z) from the Wellcome Trust outside of the submitted work. A. G. reports no potential conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.
- Published
- 2022
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45. Evidence for the intermediate disturbance hypothesis and exponential decay in replacement in Streptococcus pneumoniae following use of conjugate vaccines.
- Author
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Paulo AC and Sá-Leão R
- Subjects
- Carrier State, Child, Cross-Sectional Studies, Humans, Infant, Nasopharynx, Pneumococcal Vaccines, Serogroup, Vaccines, Conjugate, Pneumococcal Infections prevention & control, Streptococcus pneumoniae
- Abstract
Understanding how pneumococci respond to pneumococcal conjugate vaccines (PCVs) is crucial to predict the impact of upcoming higher-valency vaccines. However, stages in pneumococcal community succession following disturbance are poorly understood as long-time series on carriage are scarce and mostly evaluated at end-point measurements. We used a 20-year cross-sectional dataset of pneumococci carried by Portuguese children, and methods from community ecology, to study community assembly and diversity following use of PCV7 and PCV13. Two successional stages were detected upon introduction of each PCV: one in which non-vaccine serotypes increased in abundance, fitted by a broken-stick model, and a second in which the community returned to the original structure, fitted by a geometric series, but with different serotype profile and a drop in richness as great as 24%. A peak in diversity was observed for levels of intermediate vaccine uptake (30-40%) in agreement with the intermediate disturbance hypothesis. Serotype replacement was fitted by an exponential decay model (R
2 = 80%, P < 0.001). The half-life for replacement was 8 years for PCV7 and 10 years for PCV13. The structure of the pneumococcal community is resilient to vaccine pressure. The increasing loss of diversity, however, suggests it could eventually reach a threshold beyond which it may no longer recover., (© 2022. The Author(s).)- Published
- 2022
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46. Evaluation of Methicillin-Resistant Staphylococcus aureus Carriage in the Elderly in Portugal Using Selective Enrichment Followed by Quantitative Real-Time PCR.
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Almeida ST, Paulo AC, de Lencastre H, and Sá-Leão R
- Subjects
- Adult, Aged, Anti-Bacterial Agents pharmacology, Humans, Portugal epidemiology, Real-Time Polymerase Chain Reaction, Methicillin-Resistant Staphylococcus aureus genetics, Staphylococcal Infections epidemiology
- Abstract
The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in hospitals in Portugal is worrisome and among the highest in Europe. Surprisingly, MRSA prevalence in the community was described as very low (<2%) based on studies that used classical culture-based methods (CCBM). We investigated whether the apparent limited spread of MRSA in the community in Portugal might result from low sensitivity of CCBM. Nasopharyngeal- and oropharyngeal-paired samples obtained from senior adults living in nursing ( n = 299) or family homes ( n = 300) previously characterized by CCBM were reanalyzed. Samples were inoculated in a semi-selective enrichment medium, and those showing visible growth were evaluated by qPCR targeting nuc , mecA, and mecC genes (SSE+qPCR). By SSE+qPCR, 34 of the 1,198 (2.8%) samples were MRSA positive compared with 21 (1.8%) by CCBM. SSE+qPCR improved non-significantly detection of MRSA carriers from 5.4% to 8.0% ( p = 0.12) in the nursing home collection, and from 0.3% to 1.7% ( p = 0.13) in the family home collection. MRSA isolates belonged to three HA-MRSA clones widely disseminated in Portuguese hospitals. In conclusion, use of semi-selective medium combined with qPCR did not change the overall scenario previously described. In Portugal, MRSA circulation in the community among senior adults is low.
- Published
- 2022
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47. Intra-Species Interactions in Streptococcus pneumoniae Biofilms.
- Author
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Valente C, Cruz AR, Henriques AO, and Sá-Leão R
- Subjects
- Biofilms, Humans, Nasopharynx, Pneumococcal Infections, Streptococcus pneumoniae genetics
- Abstract
Streptococcus pneumoniae is a human pathogen responsible for high morbidity and mortality worldwide. Disease is incidental and is preceded by asymptomatic nasopharyngeal colonization in the form of biofilms. Simultaneous colonization by multiple pneumococcal strains is frequent but remains poorly characterized. Previous studies, using mostly laboratory strains, showed that pneumococcal strains can reciprocally affect each other's colonization ability. Here, we aimed at developing a strategy to investigate pneumococcal intra-species interactions occurring in biofilms. A 72h abiotic biofilm model mimicking long-term colonization was applied to study eight pneumococcal strains encompassing 6 capsular types and 7 multilocus sequence types. Strains were labeled with GFP or RFP, generating two fluorescent variants for each. Intra-species interactions were evaluated in dual-strain biofilms (1:1 ratio) using flow cytometry. Confocal microscopy was used to image representative biofilms. Twenty-eight dual-strain combinations were tested. Interactions of commensalism, competition, amensalism and neutralism were identified. The outcome of an interaction was independent of the capsular and sequence type of the strains involved. Confocal imaging of biofilms confirmed the positive, negative and neutral effects that pneumococci can exert on each other. In conclusion, we developed an experimental approach that successfully discriminates pneumococcal strains growing in mixed biofilms, which enables the identification of intra-species interactions. Several types of interactions occur among pneumococci. These observations are a starting point to study the mechanisms underlying those interactions., Competing Interests: The authors 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., (Copyright © 2022 Valente, Cruz, Henriques and Sá-Leão.)
- Published
- 2022
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48. Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time.
- Author
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Simões AS, Touret T, Faria NA, Peres Ladeiro S, Costa J, Bispo S, Serrano M, Palos C, Miragaia M, Bastos Leite R, and Sá-Leão R
- Subjects
- Anti-Bacterial Agents therapeutic use, Carbapenems pharmacology, Disease Outbreaks, Humans, Laboratories, Clinical, Microbial Sensitivity Tests, Multilocus Sequence Typing, Whole Genome Sequencing, Klebsiella Infections epidemiology, Klebsiella pneumoniae genetics
- Abstract
Introduction: Healthcare associated infections due to carbapenem-resistant Klebsiella pneumoniae (CRKP) are a major concern in Portuguese hospitals. Whole genome sequencing (WGS) can improve infection control, but this practice is not routinely used by hospital clinical laboratories in Portugal. We simulated the investigation of a CRKP outbreak based on WGS, with the aim of determining, in the minimum possible time, genetic relatedness between CRKP clinical and environmental isolates., Material and Methods: Ten CRKP clinical isolates routinely obtained in the hospital laboratory were used. Forty environmental samples - from sinks and sink drains of ward rooms - were collected. Environmental samples were plated on selective media and presumptive CRKP colonies were isolated. Total DNA was extracted from all putative CRKP isolates and sequenced. Clonal relatedness was determined by multi-locus sequence typing and core genome single nucleotide polymorphism analysis; the presence of carbapenemase genes was evaluated., Results: Clinical isolates were characterized in 48 hours: eight strains were confirmed as CRKP, of which six were of ST13 and carried blaKPC-3. Environmental samples results were obtained in six days: eight CRKP were isolated from which five were of ST13 and carried blaKPC-3. Clinical and environmental ST13 isolates were highly related: ten (of 11) isolates differed from each other in < 0.001% of 2 172 367 core nucleotides., Discussion: WGS can be used as a high-resolution effective tool to investigate healthcare associated infections and track routes of dissemination in real-time., Conclusion: In Portugal, routine use of WGS to improve infection control could thrive through collaborative initiatives between hospitals and research institutes.
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- 2022
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49. Impact of private use of the 13-valent pneumococcal conjugate vaccine (PCV13) on pneumococcal carriage among Portuguese children living in urban and rural regions.
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Félix S, Handem S, Nunes S, Paulo AC, Candeias C, Valente C, Simões AS, Almeida ST, Tavares DA, Brito-Avô A, de Lencastre H, and Sá-Leão R
- Subjects
- Carrier State epidemiology, Child, Child, Preschool, Drug Resistance, Bacterial, Humans, Infant, Infant, Newborn, Nasopharynx, Pneumococcal Vaccines, Portugal epidemiology, Serogroup, Vaccines, Conjugate, Pneumococcal Infections epidemiology, Pneumococcal Infections prevention & control
- Abstract
In Portugal, the 13-valent pneumococcal conjugate vaccine (PCV13) was commercially available between 2010 and 2015, following a decade of private use of PCV7. We evaluated changes on serotype distribution and antimicrobial susceptibility of pneumococci carried by children living in two regions of Portugal (one urban and one rural). Three epidemiological periods were defined: pre-PCV13 (2009-2010), early-PCV13 (2011-2012), and late-PCV13 (2015-2016). Nasopharyngeal samples (n = 4,232) were obtained from children 0-6 years old attending day-care centers. Private use of PCVs was very high in both regions (>75%). Pneumococcal carriage remained stable and high over time (62.1%, 62.4% and 61.6% (p = 0.909) in the urban region; and 59.8%, 62.8%, 59.5% (p = 0.543) in the rural region). Carriage of PCV7 serotypes remained low (5.3%, 7.8% and 4.3% in the urban region; and 2.5%, 3.7% and 4.8% in the rural region). Carriage of PCV13 serotypes not targeted by PCV7 decreased in both the urban (16.4%, 7.3%, and 1.6%; p < 0.001) and rural regions (13.2%, 7.8%, and 1.9%; p < 0.001). This decline was mostly attributable to serotype 19A (14.1%, 4.4% and 1.3% in the urban region; and 11.1%, 3.6% and 0.8% in the rural region, both p < 0.001). Serotype 3 declined over time in the urban region (10.1%, 4.4%, 0.8%; p < 0.001) and had no obvious trend in the rural region (4.2%, 6.7%, 2.4%; p = 0.505). Serotype 6C decreased in both regions while serotypes 11D, 15A/B/C, 16F, 21, 22F, 23A/B, 24F, 35F, and NT were the most prevalent in the late-PCV13 period. Intermediate resistance to penicillin and non-susceptibility to erythromycin decreased significantly in both regions (19.5%, 13.3%, and 9.3%; and 25.4%, 25.9%, and 13.4%; both p < 0.001, respectively in the urban region; and 12.4%, 11.1%, and 2.8% (p < 0.001); and 15.3%, 14.7%, and 9.2% (p = 0.037), respectively, in the rural region). In conclusion, private use of PCV13 led to significant changes on the pneumococcal population carried by children in Portugal., Competing Interests: Declaration of Competing Interest RSL has received consulting and speaking fees from Pfizer and consulting fees from Merck Sharp & Dome. RSL has received funds for unrestricted research grants from Pfizer, paid directly to her institution. ABA has received consulting and speaking fees from Pfizer. All other authors declare they have no conflicts of interest., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2021
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50. The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci.
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D'Aeth JC, van der Linden MP, McGee L, de Lencastre H, Turner P, Song JH, Lo SW, Gladstone RA, Sá-Leão R, Ko KS, Hanage WP, Breiman RF, Beall B, Bentley SD, and Croucher NJ
- Subjects
- DNA Transposable Elements, Genes, Bacterial genetics, Germany, Humans, Macrolides pharmacology, Phylogeny, Pneumococcal Vaccines, Serogroup, Serotyping, Streptococcus pneumoniae drug effects, Streptococcus pneumoniae genetics, Anti-Bacterial Agents pharmacology, Drug Resistance, Bacterial drug effects, Drug Resistance, Bacterial genetics, Gene Transfer, Horizontal
- Abstract
Multidrug-resistant Streptococcus pneumoniae emerge through the modification of core genome loci by interspecies homologous recombinations, and acquisition of gene cassettes. Both occurred in the otherwise contrasting histories of the antibiotic-resistant S. pneumoniae lineages PMEN3 and PMEN9. A single PMEN3 clade spread globally, evading vaccine-induced immunity through frequent serotype switching, whereas locally circulating PMEN9 clades independently gained resistance. Both lineages repeatedly integrated Tn 916 -type and Tn 1207.1 -type elements, conferring tetracycline and macrolide resistance, respectively, through homologous recombination importing sequences originating in other species. A species-wide dataset found over 100 instances of such interspecific acquisitions of resistance cassettes and flanking homologous arms. Phylodynamic analysis of the most commonly sampled Tn 1207.1 -type insertion in PMEN9, originating from a commensal and disrupting a competence gene, suggested its expansion across Germany was driven by a high ratio of macrolide-to-β-lactam consumption. Hence, selection from antibiotic consumption was sufficient for these atypically large recombinations to overcome species boundaries across the pneumococcal chromosome., Competing Interests: JD, Mv, LM, Hd, PT, JS, SL, RG, RS, KK, WH, RB, BB, SB No competing interests declared, NC has consulted for Antigen Discovery Inc Has received an investigator-initiated award from GlaxoSmithKline.
- Published
- 2021
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