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publications [2022/04/07 15:57] cmendes [2022] |
publications [2024/06/26 13:10] ramirez [2024] |
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====== Publications ====== | ====== Publications ====== | ||
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+ | Faria NA, Touret T, Simões AS, Palos C, Bispo S, [[people:jmelocristino|Melo-Cristino J]], [[people:ramirez|Ramirez M]], Carriço J, Pinto M, Toscano C, Gonçalves E, Gonçalves ML, Costa A, Araújo M, Duarte A, de Lencastre H, Serrano M, Sá-Leão R, Miragaia M. 2024. <fc #0000FF>Genomic Insights into the expansion of carbapenem-resistant //Klebsiella pneumoniae// within Portuguese Hospitals</fc>. J Hosp Infect S0195-6701(24)00106–3. [[https://www.ncbi.nlm.nih.gov/pubmed/38554808/|(PMID: 38554808)]] | ||
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+ | Xie O, Morris JM, Hayes AJ, Towers RJ, Jespersen MG, Lees JA, Ben Zakour NL, Berking O, Baines SL, Carter GP, Tonkin-Hill G, Schrieber L, McIntyre L, Lacey JA, James TB, Sriprakash KS, Beatson SA, Hasegawa T, Giffard P, Steer AC, Batzloff MR, Beall BW, [[people:mdpinho|Pinho MD]], [[people:ramirez|Ramirez M]], Bessen DE, Dougan G, Bentley SD, Walker MJ, Currie BJ, Tong SYC, McMillan DJ, Davies MR. 2024. <fc #0000FF>Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and //Streptococcus dysgalactiae// subsp. //equisimilis//</fc>. Nat Commun 15:2286. [[https://www.ncbi.nlm.nih.gov/pubmed/38480728/|(PMID: 38480728)]] | ||
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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)]] | ||
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+ | 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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+ | Bajanca-Lavado MP, Pinto M, Carvalho MD, Jantarada Domingos G, [[people:jmelocristino|Melo-Cristino J]]. 2024. <fc #0000FF>Rare serotype c //Haemophilus influenzae// invasive isolate: characterization of the first case in Portugal</fc>. Eur J Clin Microbiol Infect Dis 43:791–795 [[https://www.ncbi.nlm.nih.gov/pubmed/38332396/|(PMID: 38332396)]] | ||
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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]] | ||
+ | ===== 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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+ | Mendes G, Santos ML, Ramalho JF, Bruschy-Fonseca A, Lito L, Mendes-Pedro D, Duarte A, [[people:jmelocristino|Melo-Cristino J]], Caneiras C. 2023. <fc #0000FF>Genomic characterisation of a novel KPC-98-producing clinical //Klebsiella pneumoniae// strain conferring resistance to ceftazidime/avibactam</fc>. Int J Antimicrob Agents 62:107013. [[https://www.ncbi.nlm.nih.gov/pubmed/37875180/|(PMID: 37875180)]] | ||
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+ | Grobusch MP, Ruiz Del Portal Luyten C, Visser BJ, de Jong HK, Goorhuis A, Hanscheid T. 2023. <fc #0000FF>Overcoming publication and dissemination bias in infectious diseases clinical trials</fc>. Lancet Infect Dis S1473-3099(23)00455–3. [[https://www.ncbi.nlm.nih.gov/pubmed/37837983/|(PMID: 37837983)]] | ||
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+ | Gouveia C, Bajanca-Lavado MP, Mamede R, Araújo Carvalho A, Rodrigues F, [[people:jmelocristino|Melo-Cristino J]], [[people:ramirez|Ramirez M.]], [[people:afriaes|Friães A]], Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Pediatric Invasive Streptococcal Disease. 2023. <fc #0000FF>Sustained increase of paediatric invasive //Streptococcus pyogenes// infections dominated by M1<sub>UK</sub> and diverse //emm//12 isolates, Portugal, September 2022 to May 2023.</fc> Eurosurveillance 28(36). [[https://www.ncbi.nlm.nih.gov/pubmed/37676143/|(PMID: 37676143)]] | ||
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+ | Pinto Junior VL, Valadas E, Hanscheid T. 2023. <fc #0000FF>Combating vaccine hesitancy requires knowledge of misfortunes and controversies</fc>. Acta Med Port 36:537–540. [[https://pubmed.ncbi.nlm.nih.gov/37579748/|(PMID: 37579748)]] | ||
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+ | Riche CVW, Cassol R, Falci DR, [[people:ramirez|Ramirez M]], Dias CAG. 2023. <fc #0000FF>Epidemiology and risk factors for mortality among methicillin-resistant //Staphylococcus aureus// bacteremic patients in Southern Brazil</fc>. PLoS One 18:e0283774. [[https://pubmed.ncbi.nlm.nih.gov/37053222/|(PMID: 37053222)]] | ||
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+ | Marinho PF, Vieira SL, Carvalho TG, Peleteiro MC, Hanscheid T. 2023. <fc #0000FF>A novel and simple heat-based method eliminates the highly detrimental effect of xylene deparaffinization on acid-fast stains</fc>. Am J Clin Pathol 160:81–88. [[https://pubmed.ncbi.nlm.nih.gov/36897250/|(PMID: 36897250)]] | ||
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+ | Bouchami O, Machado M, [[people:jcarrico|Carriço JA]], [[people:jmelocristino|Melo-Cristino J]], de Lencastre H, Miragaia M. 2023. <fc #0000FF>Spontaneous genomic variation as a survival strategy of nosocomial //Staphylococcus haemolyticus//</fc>. Microbiol Spectr 11:e0255222. [[https://pubmed.ncbi.nlm.nih.gov/36877037/|(PMID: 36877037)]] | ||
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+ | Marinho PF, Hanscheid T. 2023. <fc #0000FF>A simple heat-based alternative method for deparaffinization of histological sections significantly improves acid-fast staining results for Mycobacteria in tissue</fc>. MethodsX 10:102079. [[https://pubmed.ncbi.nlm.nih.gov/36865652/|(PMID: 36865652)]] | ||
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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)]] | ||
===== 2022 ===== | ===== 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)]] | ||
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+ | Kalkman LC, Hänscheid T, Krishna S, Grobusch MP. 2022. <fc #0000FF>Fluid therapy in sepsis? Pathogen-specific perspectives</fc>. New Microbes New Infect 49–50:101035. [[https://pubmed.ncbi.nlm.nih.gov/36324876/|(PMID: 36324876)]] | ||
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+ | Kalkman LC, Hanscheid T, Krishna S, Kremsner PG, Grobusch MP. 2022. <fc #0000FF>Antimalarial treatment in infants</fc>. Expert Opin Pharmacother 23:1711–1726. [[https://pubmed.ncbi.nlm.nih.gov/36174125/|(PMID: 36174125)]] | ||
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+ | Hernández-García M, García-Castillo M, [[people:jmelocristino|Melo-Cristino J]], Pinto MF, Gonçalves E, Alves V, Vieira AR, Ramalheira E, Sancho L, Diogo J, Ferreira R, Cruz H, Chaves C, Bou G, Cercenado E, Delgado-Valverde M, Oliver A, Pitart C, Rodríguez-Lozano J, Tormo N, Díaz-Regañón J, Pássaro L, Duarte J, Cantón R, STEP and SUPERIOR study groups. 2022. <fc #0000FF>In vitro activity of imipenem/relebactam against Pseudomonas aeruginosa isolates recovered from ICU patients in Spain and Portugal (SUPERIOR and STEP studies)</fc>. J Antimicrob Chemother 77:3163–3172. [[https://pubmed.ncbi.nlm.nih.gov/36059128/|(PMID: 36059128)]] | ||
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+ | Hernández-García M, García-Castillo M, Bou G, Cercenado E, Delgado-Valverde M, Oliver A, Pitart C, Rodríguez-Lozano J, Tormo N, [[people:jmelocristino|Melo-Cristino J]], Pinto MF, Gonçalves E, Alves V, Vieira AR, Ramalheira E, Sancho L, Diogo J, Ferreira R, Cruz H, Chaves C, Duarte J, Pássaro L, Díaz-Regañón J, Cantón R. 2022. <fc #0000FF>Imipenem-Relebactam Susceptibility in Enterobacterales Isolates Recovered from ICU Patients from Spain and Portugal (SUPERIOR and STEP Studies)</fc>. Microbiol Spectr 10:e0292722. [[https://pubmed.ncbi.nlm.nih.gov/36043877/|(PMID: 36043877)]] | ||
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+ | [[people:anacosta|Silva-Costa C]], Gomes-Silva J, [[people:mdpinho|Pinho MD]], [[people:afriaes|Friães A]], [[people:ramirez|Ramirez M.]], [[people:jmelocristino|Melo-Cristino J]]. 2022. <fc #0000FF>Continued Vaccine Breakthrough Cases of Serotype 3 Complicated Pneumonia in Vaccinated Children, Portugal (2016-2019)</fc>. Microbiol Spectr. 2022 Aug 31;10(4):e0107722.[[https://pubmed.ncbi.nlm.nih.gov/35862941/|(PMID: 35862941)]] | ||
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+ | Mukherjee D, Chora ÂF, Lone J-C, Ramiro RS, Blankenhaus B, Serre K, [[people:ramirez|Ramirez M.]], Gordo I, Veldhoen M, Varga-Weisz P, Mota MM. 2022. <fc #0000FF>lung microbiota promotes malaria-associated acute respiratory distress syndrome</fc>. Nat Commun 13:3747.[[http://www.ncbi.nlm.nih.gov/pubmed/35768411/|(PMID: 35768411)]] | ||
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+ | Schnyder JL, de Jong HK, Schlagenhauf P, Borrmann S, Hanscheid T, Grobusch MP. 2022. <fc #0000FF>Discontinuing atovaquone/proguanil prophylaxis ad-hoc post-exposure and during-travel dose-sparing prophylactic regimens against //P. falciparum// malaria: An update with pointers for future research</fc>. Travel Med Infect Dis 49:102365. [[http://www.ncbi.nlm.nih.gov/pubmed/35661741/|(PMID: 35661741)]] | ||
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+ | [[people:emartins|Martins ER]], Nascimento do Ó D, Marques Costa AL, [[people:jmelocristino|Melo-Cristino J]], [[people:ramirez|Ramirez M.]] 2022. <fc #0000FF>Characteristics of //Streptococcus agalactiae// colonizing nonpregnant adults support the opportunistic nature of invasive infections</fc>. Microbiol Spectr 10:e0108222. [[http://www.ncbi.nlm.nih.gov/pubmed/35604173/|(PMID: 35604173)]] | ||
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+ | [[people:afriaes|Friães A]], Mamede R, Ferreira M, [[people:jmelocristino|Melo-Cristino J]], [[people:ramirez|Ramirez M.]] 2022. <fc #0000FF>Annotated whole-genome multilocus sequence typing schema for scalable high-resolution typing of //Streptococcus pyogenes//</fc>. J Clin Microbiol 60:e0031522. [[http://www.ncbi.nlm.nih.gov/pubmed/35531659/|(PMID: 35531659)]] | ||
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+ | Elias R, Spadar A, Phelan J, [[people:jmelocristino|Melo-Cristino J]], Lito L, Pinto M, Gonçalves L, Campino S, Clark TG, Duarte A, Perdigão J. 2022. <fc #0000FF>A phylogenomic approach for the analysis of colistin resistance-associated genes in //Klebsiella pneumoniae//, its mutational diversity and implications for phenotypic resistance</fc>. Int J Antimicrob Agents 59:106581. | ||
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+ | Ricci ML, Fillo S, Ciammaruconi A, Lista F, Ginevra C, Jarraud S, Girolamo A, Barbanti F, Rota MC, Lindsay D, Gorzynski J, Uldum SA, Baig S, Foti M, Petralito G, Torri S, Faccini M, Bonini M, Gentili G, Senatore S, Lamberti A, [[people:jcarrico|Carriço JA]], Scaturro M. 2022. <fc #0000FF>Genome analysis of //Legionella pneumophila// ST23 from various countries reveals highly similar strains</fc>. Life Sci Alliance 5:e202101117. [[http://www.ncbi.nlm.nih.gov/pubmed/35236759/|(PMID: 35236759)]] | ||
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+ | Mendes G, Ramalho JF, Bruschy-Fonseca A, Lito L, Duarte A, [[people:jmelocristino|Melo-Cristino J]], Caneiras C. 2022. <fc #0000FF>Whole-Genome Sequencing Enables Molecular Characterization of Non-Clonal Group 258 High-Risk Clones (ST13, ST17, ST147 and ST307) among Carbapenem-Resistant //Klebsiella pneumoniae// from a Tertiary University Hospital Centre in Portugal</fc>. Microorganisms 10:416. [[http://www.ncbi.nlm.nih.gov/pubmed/35208876/|(PMID: 35208876)]] | ||
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+ | Mendes G, Ramalho JF, Bruschy-Fonseca A, Lito L, Duarte A, [[people:jmelocristino|Melo-Cristino J]], Caneiras C. 2022. <fc #0000FF>First Description of Ceftazidime/Avibactam Resistance in a ST13 KPC-70-Producing //Klebsiella pneumoniae// Strain from Portugal</fc>. Antibiotics (Basel) 11:167. [[http://www.ncbi.nlm.nih.gov/pubmed/35203770/|(PMID: 35203770)]] | ||
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Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan N-F, Fornika D, Maguire F, Campos J, Park D, Olawoye IB, Oluniyi PE, Anderson D, Christoffels A, da Silva AG, Cameron R, Dooley D, Katz LS, Black A, Karsch-Mizrachi I, Barrett T, Johnston A, Connor TR, Nicholls SM, Witney AA, Tyson GH, Tausch SH, Raphenya AR, Alcock B, Aanensen DM, Hodcroft E, Hsiao WWL, Vasconcelos ATR, MacCannell DR. 2022. <fc #0000FF>Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package</fc>. Gigascience 11:giac003 [[http://www.ncbi.nlm.nih.gov/pubmed/35169842/|(PMID: 35169842)]] | Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan N-F, Fornika D, Maguire F, Campos J, Park D, Olawoye IB, Oluniyi PE, Anderson D, Christoffels A, da Silva AG, Cameron R, Dooley D, Katz LS, Black A, Karsch-Mizrachi I, Barrett T, Johnston A, Connor TR, Nicholls SM, Witney AA, Tyson GH, Tausch SH, Raphenya AR, Alcock B, Aanensen DM, Hodcroft E, Hsiao WWL, Vasconcelos ATR, MacCannell DR. 2022. <fc #0000FF>Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package</fc>. Gigascience 11:giac003 [[http://www.ncbi.nlm.nih.gov/pubmed/35169842/|(PMID: 35169842)]] | ||
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Barros Pinto MP, Marques G, [[people:jmelocristino|Melo-Cristino J]]. 2021 <fc #0000FF>Promastigotes of //Leishmania// spp. developing in human bone marrow in vitro</fc>. Br J Haematol 192:7. [[http://www.ncbi.nlm.nih.gov/pubmed/32945533|(PMID: 32945533)]] | Barros Pinto MP, Marques G, [[people:jmelocristino|Melo-Cristino J]]. 2021 <fc #0000FF>Promastigotes of //Leishmania// spp. developing in human bone marrow in vitro</fc>. Br J Haematol 192:7. [[http://www.ncbi.nlm.nih.gov/pubmed/32945533|(PMID: 32945533)]] | ||
+ | Vaz C, Nascimento M, [[people:jcarrico|Carriço JA]], Rocher T, Francisco AP. 2020. <fc #0000FF>Distance-based phylogenetic inference from typing data: a unifying view</fc>. Brief Bioinformatics 22:bbaa147. [[http://www.ncbi.nlm.nih.gov/pubmed/32734294|(PMID: 32734294)]] | ||
===== 2020 ===== | ===== 2020 ===== | ||
Utzinger KS, Held U, Hänscheid T, Gültekin N, Fehr J, Grobusch MP, Schlagenhauf P. 2020. <fc #0000FF>Self-diagnosis and self-treatment of //Plasmodium// spp. infection by travellers (1989-2019): A systematic review and meta-analysis</fc>. Travel Med Infect Dis 38:101902. [[http://www.ncbi.nlm.nih.gov/pubmed/33132136|(PMID: 33132136)]] | Utzinger KS, Held U, Hänscheid T, Gültekin N, Fehr J, Grobusch MP, Schlagenhauf P. 2020. <fc #0000FF>Self-diagnosis and self-treatment of //Plasmodium// spp. infection by travellers (1989-2019): A systematic review and meta-analysis</fc>. Travel Med Infect Dis 38:101902. [[http://www.ncbi.nlm.nih.gov/pubmed/33132136|(PMID: 33132136)]] |