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--- publications [2025/03/24 20:24]
ramirez [2023]
+++ publications [2025/12/04 11:01] (current)
ramirez [2025]
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 ===== 2025  =====
-[[people:afriaes|Friães A]], Mamede R, Santos B, [[people:jmelocristino|Melo-Cristino J]], [[people:ramirez|Ramirez M]], Portuguese Group for the Study of Streptococcal Infections. 2025. <fc #0000FF>Characteristics of //Streptococcus pyogenes// causing invasive infections among adults in Portugal, 2016-2019: Pre-COVID-19 expansion of the M1UK sublineage</fc>. J Microbiol Immunol Infect S1684-1182(25)33–7. [[https://www.ncbi.nlm.nih.gov/pubmed/40021403/|(PMID: 40021403)]]
+Boto CM, Raposo Carneiro S, Ramalho M, Passos Coelho I, Moitinho de Almeida I, Ferreira C, Tomé ML, Sousa Dias M, Araújo Carvalho A, Machado R, Oliveira M, Seruca M, Boto L, Prata F, Penteado R, Carmo A, Rodrigues F, Tavares M, Rebelo S, Ribeiro M, [[people:jfsilva|Gomes-Silva J]], [[people:afriaes|Friães A]], [[people:anacosta|Silva-Costa C]], [[people:ramirez|Ramirez M]], [[people:jmelocristino|Melo-Cristino J]], Pereira Lemos A, Gouveia C. 2025. <fc #0000FF>Increasingly frequent parapneumonic empyema by group A streptococcus is more severe than by //Streptococcus pneumoniae//</fc>. Pediatr Infect Dis J //In press// [[https://www.ncbi.nlm.nih.gov/pubmed/41334964/|(PMID: 41334964)]].
-Couto C, Pereira Lemos A, Stella L, Sobral C, Marques J, [[people:afriaes|Friães A]], [[people:jfsilva|Gomes-Silva J]], Gouveia C. 2025. <fc #0000FF>Myositis and deep suppurative soft tissue infections caused by group A streptococcus</fc>. Pediatr Infect Dis J //in press// [[https://www.ncbi.nlm.nih.gov/pubmed/39999353/|(PMID: 39999353)]]
+Guerreiro-Nunes A, [[people:anacosta|Silva-Costa C]], [[people:jfsilva|Gomes-Silva J]], [[people:ramirez|Ramirez M]], [[people:jmelocristino|Melo-Cristino J]], Portuguese Group for the Study of Streptococcal Infections. 2025. <fc #0000FF>The resilience of vaccine serotypes in adult invasive pneumococcal disease in Portugal, 2018-2023</fc>. Sci Rep 15:40146. [[https://www.ncbi.nlm.nih.gov/pubmed/41249230/|(PMID: 41249230)]].
+Lenglart L, Özmen I, Aguilera-Alonso D, Blazquez-Gamero D, Boeddha NP, Buddingh EP, Buonsenso D, Calvo C, Castagnoli R, Daina M, Dourdouna M-M, Emonts M, Ezinwoke C, Gouveia C, Vas DG, Hol J, Holm M, Kahlert CR, Kohlmaier B, Ludwikowska K, Marseglia GL, McArdle A, McGalliard R, Michos A, Nagle A, Niederer-Loher A, Nygaard U, Oostenbrink R, Srovin TP, Roisin S, Saavedra-Lozano J, Shan A, Thors VS, Strenger V, Syngelou A, Tilmanne A, Tokarczyk M, Tsilifis C, Tsolia M, Tulling A, van Kempen E, Van Veen M, Vincek K, Von Both U, Zavadska D, Zaman M, Nijman RG, Ouldali N, Borensztajn D, Lenglart L, Özmen I, Aguilera-Alonso D, Blazquez-Gamero D, Boeddha NP, Buddingh EP, Buonsenso D, Calvo C, Castagnoli R, Daina M, Dourdouna M-M, Emonts M, Ezinwoke C, Gouveia C, Vas DG, Hol J, Holm M, Kahlert CR, Kohlmaier B, Ludwikowska K, Marseglia GL, McArdle A, McGalliard R, Michos A, Nagle A, Niederer-Loher A, Nygaard U, Oostenbrink R, Srovin TP, Roisin S, Saavedra-Lozano J, Shan A, Thors VS, Strenger V, Syngelou A, Tilmanne A, Tokarczyk M, Tsilifis C, Tsolia M, Tulling A, van Kempen E, Van Veen M, Vincek K, Von Both U, Zavadska D, Zaman M, Nijman RG, Ouldali N, Borensztajn D, Dekkers F, Giske C, Hawkins R, Hertting O, Kolnik M, Carrol E, Lewis-Burke N, Pokorn M, Raghoenath P, Rhedin S, Rozemeijer W, Seme K, Syrimi N, Tatsi E-B, Velimirovic I, Wilfing S, Till H, Ramirez M, Friães A. 2025. <fc #0000FF>Paediatric invasive group A streptococcal infections and associations with viral infections in 15 European countries after lifting non-pharmaceutical interventions against SARS-CoV-2: an interrupted time-series analysis</fc>. Lancet Reg Health - Eur 59:101497. [[https://www.ncbi.nlm.nih.gov/pubmed/41170145/|(PMID: 41170145)]].
+[[people:afriaes|Friães A]], Mamede R, Santos B, Marrão G, [[people:jmelocristino|Melo-Cristino J]], [[people:ramirez|Ramirez M]]. 2025. <fc #0000FF>Increase of macrolide resistance among //Streptococcus pyogenes// pharyngitis driven by a //mef//(A)-//msr//(D)///emm//2-ST55 lineage in Portugal (2014-2019)</fc>. Antimicrob Agents Chemother 69:e0096825. [[https://www.ncbi.nlm.nih.gov/pubmed/41071123/|(PMID: 41071123)]]
+Firmino M de O, Forofontov M, Soares R, Louro RO, Alberto J. Martín-Rodríguez, [[people:ramirez|Ramirez M]], Paquete CM. 2025. <fc #0000FF>Polyphasic discrimination of //Shewanella seohaensis// from closely related species and a whole-genome multilocus (wgMLST) scheme for the evaluation of diversity within this //Shewanella// clade</fc>. Appl Environ Microbiol 91:e0118925. [[https://www.ncbi.nlm.nih.gov/pubmed/40801780/|(PMID: 40801780)]]
+Boattini M, Aceti A, Bastos P, Mavromanolaki VE, Maraki S, Spiliopoulou A, Kakouris V, Kalchev Y, Budimir A, Bedenić B, Rubic Z, Licker M, Musuroi C, Juhász E, Kristóf K, Pirs M, Velimirovic I, Berktold M, Liptáková A, Krajčíková A, Drevinek P, Gryndlerova A, Brzychczy-Wloch M, Olechowska-Jarząb A, Bielec F, Brauncajs M, Podsiadly E, Nurzyńska G, Zalas-Więcek P, Michalska A, Riesbeck K, Andersson H-S, Tønjum T, Berild JC, Leegaard TM, Rasmussen AN, Schønning K, Glöckner S, Rödel J, Badr MT, Häcker GA, Stark D, Hamprecht A, Dudakova A, Jantsch J, Mancini S, Quiblier C, Jacot D, Greub G, Ferniani T, Ambretti S, Calvo M, Stefani S, Schade R, Yusuf E, van Kleef-van Koeveringe S, Vandamme S, Verroken A, Rodriguez-Villalobos H, Duigou F, Corvec S, Floch P, Massip C, Chainier D, Barraud O, Louissaint M-B, Mizrahi A, Ali S, Doyle M, Egan C, McNicholas S, Colomina-Rodriguez J, Torres I, Gillaranz Luengo R, Larrosa Escartín MN, Viñado Perez MB, Halperin AV, Fuente García S, Cantón R, Seruca M, Santos Mendes V, Carvalho D, Cavallo R, [[people:jmelocristino|Melo-Cristino J]], Costa C, Bianco G. 2025. <fc #0000FF>A european survey on anaerobes from paediatric blood cultures: a comparative analysis with adults</fc>. Eur J Clin Microbiol Infect Dis 44:2207–2217. [[https://www.ncbi.nlm.nih.gov/pubmed/40537731/|(PMID: 40537731)]]
+Stanley S, [[people:anacosta|Silva-Costa C]], [[people:jfsilva|Gomes-Silva J]], [[people:jmelocristino|Melo-Cristino J]], Malley R, [[people:ramirez|Ramirez M]]. 2025. <fc #0000FF>CC180 clade dynamics do not universally explain //Streptococcus pneumoniae// serotype 3 persistence post-vaccine: a global comparative population genomics study</fc>. Ebiomedicine 117:105781. [[https://www.ncbi.nlm.nih.gov/pubmed/40472804/|(PMID: 40472804)]]
+Carvalho BT, Meirinhos SV, Domingos GJ, Peixoto S, [[people:jmelocristino|Melo-Cristino J]]. 2025. <fc #0000FF>Unseen but unforgettable - refractive bacilli in the Gram stain of a muscular abscess</fc>. Eur J Clin Microbiol Infect Dis //In press// [[https://www.ncbi.nlm.nih.gov/pubmed/40307630/|(PMID: 40307630)]]
+Boattini M, Bianco G, Bastos P, Mavromanolaki VE, Maraki S, Spiliopoulou A, Kakouris V, Kalchev Y, Budimir A, Bedenić B, Rubic Z, Licker M, Musuroi C, Juhász E, Kristóf K, Pirs M, Velimirovic I, Berktold M, Liptáková A, Krajcikova A, Drevinek P, Gryndlerova A, Brzychczy-Wloch M, Olechowska-Jarząb A, Bielec F, Brauncajs M, Podsiadly E, Nurzyńska G, Zalas-Więcek P, Riesbeck K, Andersson H-S, Tønjum T, Berild JC, Leegaard TM, Rasmussen AN, Schønning K, Glöckner S, Rödel J, Badr MT, Häcker GA, Stark D, Hamprecht A, Dudakova A, Jantsch J, Mancini S, Quiblier C, Jacot D, Greub G, Ferniani T, Ambretti S, Calvo M, Stefani S, Schade R, Yusuf E, Koeveringe S van K, Vandamme S, Verroken A, Rodriguez-Villalobos H, Duigou F, Corvec S, Floch P, Massip C, Chainier D, Barraud O, Louissaint M-B, Mizrahi A, Ali S, Doyle M, Egan C, McNicholas S, Colomina-Rodriguez J, Torres I, Luengo RG, Escartín MNL, Perez MBV, Halperin AV, García SF, Cantón R, Seruca M, Mendes VS, Carvalho D, Cavallo R, [[people:jmelocristino|Melo-Cristino J]], Costa C. 2025. <fc #0000FF>Diagnostic and epidemiological landscape of anaerobic bacteria in Europe, 2020-2023 (ANAEuROBE)</fc>. Int J Antimicrob Agents 65:107478. [[https://www.ncbi.nlm.nih.gov/pubmed/40024606/|(PMID: 40024606)]]
+[[people:afriaes|Friães A]], Mamede R, Santos B, [[people:jmelocristino|Melo-Cristino J]], [[people:ramirez|Ramirez M]], Portuguese Group for the Study of Streptococcal Infections. 2025. <fc #0000FF>Characteristics of //Streptococcus pyogenes// causing invasive infections among adults in Portugal, 2016-2019: Pre-COVID-19 expansion of the M1UK sublineage</fc>. J Microbiol Immunol Infect 58:333–339. [[https://www.ncbi.nlm.nih.gov/pubmed/40021403/|(PMID: 40021403)]]
+Couto C, Pereira Lemos A, Stella L, Sobral C, Marques J, [[people:afriaes|Friães A]], [[people:jfsilva|Gomes-Silva J]], Gouveia C. 2025. <fc #0000FF>Myositis and deep suppurative soft tissue infections caused by group A streptococcus</fc>. Pediatr Infect Dis J 44:e224-e225 [[https://www.ncbi.nlm.nih.gov/pubmed/39999353/|(PMID: 39999353)]]
 Venâncio de Barros A, Sousa Gonçalves F, Mendonça L, Carvalho D, [[people:jmelocristino|Melo-Cristino J]]. 2025. <fc #0000FF>//Histoplasma capsulatum// var. //duboisii//: a case of histoplasmosis 50 years after the exposure</fc>. Cureus 17:e77854. [[https://www.ncbi.nlm.nih.gov/pubmed/39991370/|(PMID: 39991370)]]
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 Hänscheid T, Grobusch MP. 2024. <fc #0000FF>Is strong AI skepticism justified or counterproductive?</fc> Clin Infect Dis ciae443. //In press// [[https://www.ncbi.nlm.nih.gov/pubmed/39219480/|(PMID: 39219480)]]
-Stanley S, [[people:anacosta|Silva-Costa C]], [[people:jfsilva|Gomes-Silva J]], [[people:jmelocristino|Melo-Cristino J]], Malley R, [[people:ramirez|Ramirez M]]. 2024. <fc #0000FF>CC180 clade dynamics does not universally explain //Streptococcus pneumoniae// serotype 3 persistence post-vaccine: a global comparative population genomics study</fc>. medRxiv [[https://doi.org/10.1101/2024.08.29.24312665|(doi: 10.1101/2024.08.29.24312665)]]
 Barros Pinto MP. 2024. <fc #0000FF>//Bordetella pertussis// infection</fc>. Pediatr Pulmonol 59:3752–3753. [[https://www.ncbi.nlm.nih.gov/pubmed/39189943/|(PMID: 39189943)]]
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 Mendes Pedro D, Paulo SE, Santos CM, Fonseca AB, [[people:jmelocristino|Melo-Cristino J]], Pereira AA, Caneiras C. 2024. <fc #0000FF>Extensively drug-resistant //Pseudomonas aeruginosa//: clinical features and treatment with ceftazidime/avibactam and ceftolozane/tazobactam in a tertiary care university hospital center in Portugal – A cross-sectional and retrospective observational study</fc>. Frontiers in Microbiology 15. 15:1347521. [[https://www.ncbi.nlm.nih.gov/pubmed/38414772/|(PMID: 38414772)]]
+Brandão N, Jesus A, Páscoa A, Francisco AP, [[people:ramirez|Ramirez M]], Vaz C. 2024. <fc #0000FF>A modular and scalable web platform for computational phylogenetics</fc>. arXiv:2405.16346. arXiv [[https://doi.org/10.48550/arXiv.2405.16346|doi:10.48550/arXiv.2405.16346]]
 Boattini M, Bianco G, Llorente LI, Acero LA, Nunes D, Seruca M, Mendes VS, Almeida A, Bastos P, Rodríguez-Villodres Á, Gascón AG, Halperin AV, Cantón R, Escartín MNL, González-López JJ, Floch P, Massip C, Chainier D, Barraud O, Dortet L, Cuzon G, Zancanaro C, Mizrahi A, Schade R, Rasmussen AN, Schønning K, Hamprecht A, Schaffarczyk L, Glöckner S, Rödel J, Kristóf K, Balonyi Á, Mancini S, Quiblier C, Fasciana T, Giammanco A, Paglietti B, Rubino S, Budimir A, Bedenić B, Rubic Z, Marinović J, Gartzonika K, Christaki E, Mavromanolaki VE, Maraki S, Yalçın TY, Azap ÖK, Licker M, Musuroi C, Talapan D, Vrancianu CO, Comini S, Zalas-Więcek P, Michalska A, Cavallo R, [[people:jmelocristino|Melo-Cristino J]], Costa C. 2024. <fc #0000FF>Enterobacterales carrying chromosomal AmpC β-lactamases in Europe (EuESCPM): Epidemiology and antimicrobial resistance burden from a cohort of 27 hospitals, 2020-2022</fc>. Int J Antimicrob Agents 63:107115. [[https://www.ncbi.nlm.nih.gov/pubmed/38367844/|(PMID: 38367844)]]
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 [[people:anacosta|Silva-Costa C]], [[people:jmelocristino|Melo-Cristino J]], [[people:ramirez|Ramirez M.]] 2024. <fc #0000FF>//Streptococcus pneumoniae//</fc>, p. 1479–1490. In Tang, Y-W, Hindiyeh, MY, Liu, D, Sails, A, Spearman, P, Zhang, J-R (eds.), Molecular Medical Microbiology (Third Edition). Academic Press. [[https://doi.org/10.1016/B978-0-12-818619-0.00095-2|doi:10.1016/B978-0-12-818619-0.00095-2]][[https://www.sciencedirect.com/science/article/abs/pii/B9780128186190000952
 |Publisher site]]
+Grobusch MP, Ruiz Del Portal Luyten C, Visser BJ, de Jong HK, Goorhuis A, Hanscheid T. 2024. <fc #0000FF>Overcoming publication and dissemination bias in infectious diseases clinical trials</fc>. Lancet Infect Dis 24:e189-e195. [[https://www.ncbi.nlm.nih.gov/pubmed/37837983/|(PMID: 37837983)]]
 ===== 2023  =====
 [[people:anacosta|Silva-Costa C]], Gomes-Silva J, Santos A, [[people:ramirez|Ramirez M]], [[people:jmelocristino|Melo-Cristino J]], The Portuguese Group for the Study of Streptococcal Infections. 2023. <fc #0000FF>Adult non-invasive pneumococcal pneumonia in Portugal is dominated by serotype 3 and non-PCV13 serotypes 3-years after near universal PCV13 use in children</fc>. Frontiers in Public Health 11:1279656 [[https://www.ncbi.nlm.nih.gov/pubmed/38186693/|(PMID: 38186693)]]
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 Schnyder JL, de Jong HK, Bache EB, van Hest RM, Schlagenhauf P, Borrmann S, Hanscheid T, Grobusch MP. 2023. <fc #0000FF>On the potential for discontinuing atovaquone-proguanil (AP) ad-hoc post-exposure and other abbreviated AP-regimens: Pharmacology, pharmacokinetics and perspectives</fc>. Travel Med Infect Dis 52: //In press// [[https://pubmed.ncbi.nlm.nih.gov/36526126/|(PMID: 36526126)]]
-Grobusch MP, Ruiz Del Portal Luyten C, Visser BJ, de Jong HK, Goorhuis A, Hanscheid T. 2024. <fc #0000FF>Overcoming publication and dissemination bias in infectious diseases clinical trials</fc>. Lancet Infect Dis 24:e189-e195. [[https://www.ncbi.nlm.nih.gov/pubmed/37837983/|(PMID: 37837983)]]
 ===== 2022  =====
 Mendes CI, Vila-Cerqueira P, Motro Y, Moran-Gilad J, [[people:jcarrico|Carriço JA]], [[people:ramirez|Ramirez M.]]. 2022. <fc #0000FF>LMAS: evaluating metagenomic short de novo assembly methods through defined communities</fc>. Gigascience 12:giac122. [[https://pubmed.ncbi.nlm.nih.gov/36576131/|(PMID: 36576131)]]