Publications

Gomes-Silva J, Pinho MD, Friães A, Ramirez M, Melo-Cristino J, Silva-Costa C, Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Invasive Pneumococcal Disease of the Pediatric Infectious Disease Society. 2024. Pneumococci remain the main cause of complicated pediatric pneumonia in the post-pandemic era despite extensive pneumococcal vaccine use. Pneumonia 16:26. (PMID: 39582053)

Nunes D, Luís F, Flores MAQ, Ribeiro C, Vaz Carneiro C, Melo-Cristino J. 2024. Co-Infectious Mystery: Why artemether-lumefantrine cleared P. falciparum but left P. malariae behind. Indian J Hematol Blood Transfus 40:737–738.(PMID: 39469162)

Pool L, Ruiz Del Portal Luyten C, van der Pluijm RW, Soentjens P, Hänscheid T, Grobusch MP, Visser BJ. 2024. Dissemination and outcome reporting bias in clinical malaria intervention trials: a cross-sectional analysis. Malar J 23:293. (PMID: 39350104)

Hänscheid T, Grobusch MP. 2024. Is strong AI skepticism justified or counterproductive? Clin Infect Dis ciae443. In press (PMID: 39219480)

Stanley S, Silva-Costa C, Gomes-Silva J, Melo-Cristino J, Malley R, Ramirez M. 2024. CC180 clade dynamics does not universally explain Streptococcus pneumoniae serotype 3 persistence post-vaccine: a global comparative population genomics study. medRxiv (doi: 10.1101/2024.08.29.24312665)

Mutschler E, Roloff T, Neves A, Aamot HV, Rodriguez-Sanchez B, Ramirez M, Rossen J, Couto N, Novais Â, Howden BP, Brisse S, Reuter S, Nolte O, Egli A, Seth-Smith HMB. 2024. Towards unified reporting of genome sequencing results in clinical microbiology. PeerJ 12:e17673. (PMID: 39131622)

Silva-Costa C, Gomes-Silva J, Pinho MD, Friães A, Subtil-Limpo F, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections and the Portuguese Study Group of Invasive Pneumococcal Disease of the Pediatric Infectious Disease Society. 2024. Rebound of pediatric invasive pneumococcal disease in Portugal after the COVID-19 pandemic was not associated with significant serotype changes. J Infect 89:106242. (PMID: 39116949)

Quadros Flores MA, Volovetska Y, Marques T, Melo-Cristino J. 2024. Are these lesions contagious? Enferm Infecc Microbiol Clin S2529-993X(24)00113–8. (PMID: 38705752)

Hänscheid T, Del Portal Luyten CR, Hermans SM, Grobusch MP. 2024. Repurposing of anti-malarial drugs for the treatment of tuberculosis: realistic strategy or fanciful dead end? Malar J 23:132. (PMID: 38702649)

Faria NA, Touret T, Simões AS, Palos C, Bispo S, Melo-Cristino J, 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. Genomic Insights into the expansion of carbapenem-resistant Klebsiella pneumoniae within Portuguese Hospitals. J Hosp Infect S0195-6701(24)00106–3. (PMID: 38554808)

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, Pinho MD, Ramirez M, Bessen DE, Dougan G, Bentley SD, Walker MJ, Currie BJ, Tong SYC, McMillan DJ, Davies MR. 2024. Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis. Nat Commun 15:2286. (PMID: 38480728)

Mendes Pedro D, Paulo SE, Santos CM, Fonseca AB, Melo-Cristino J, Pereira AA, Caneiras C. 2024. 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. Frontiers in Microbiology 15. 15:1347521. (PMID: 38414772)

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, Melo-Cristino J, Costa C. 2024. Enterobacterales carrying chromosomal AmpC β-lactamases in Europe (EuESCPM): Epidemiology and antimicrobial resistance burden from a cohort of 27 hospitals, 2020-2022. Int J Antimicrob Agents 63:107115. (PMID: 38367844)

Bajanca-Lavado MP, Pinto M, Carvalho MD, Jantarada Domingos G, Melo-Cristino J. 2024. Rare serotype c Haemophilus influenzae invasive isolate: characterization of the first case in Portugal. Eur J Clin Microbiol Infect Dis 43:791–795 (PMID: 38332396)

Silva-Costa C, Melo-Cristino J, Ramirez M. 2024. Streptococcus pneumoniae, 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. doi:10.1016/B978-0-12-818619-0.00095-2Publisher site

Silva-Costa C, Gomes-Silva J, Santos A, Ramirez M, Melo-Cristino J, The Portuguese Group for the Study of Streptococcal Infections. 2023. 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. Frontiers in Public Health 11:1279656 (PMID: 38186693)

Mendes G, Santos ML, Ramalho JF, Bruschy-Fonseca A, Lito L, Mendes-Pedro D, Duarte A, Melo-Cristino J, Caneiras C. 2023. Genomic characterisation of a novel KPC-98-producing clinical Klebsiella pneumoniae strain conferring resistance to ceftazidime/avibactam. Int J Antimicrob Agents 62:107013. (PMID: 37875180)

Grobusch MP, Ruiz Del Portal Luyten C, Visser BJ, de Jong HK, Goorhuis A, Hanscheid T. 2023. Overcoming publication and dissemination bias in infectious diseases clinical trials. Lancet Infect Dis S1473-3099(23)00455–3. (PMID: 37837983)

Gouveia C, Bajanca-Lavado MP, Mamede R, Araújo Carvalho A, Rodrigues F, Melo-Cristino J, Ramirez M., Friães A, Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Pediatric Invasive Streptococcal Disease. 2023. Sustained increase of paediatric invasive Streptococcus pyogenes infections dominated by M1_UK and diverse emm12 isolates, Portugal, September 2022 to May 2023. Eurosurveillance 28(36). (PMID: 37676143)

Pinto Junior VL, Valadas E, Hanscheid T. 2023. Combating vaccine hesitancy requires knowledge of misfortunes and controversies. Acta Med Port 36:537–540. (PMID: 37579748)

Riche CVW, Cassol R, Falci DR, Ramirez M, Dias CAG. 2023. Epidemiology and risk factors for mortality among methicillin-resistant Staphylococcus aureus bacteremic patients in Southern Brazil. PLoS One 18:e0283774. (PMID: 37053222)

Marinho PF, Vieira SL, Carvalho TG, Peleteiro MC, Hanscheid T. 2023. A novel and simple heat-based method eliminates the highly detrimental effect of xylene deparaffinization on acid-fast stains. Am J Clin Pathol 160:81–88. (PMID: 36897250)

Bouchami O, Machado M, Carriço JA, Melo-Cristino J, de Lencastre H, Miragaia M. 2023. Spontaneous genomic variation as a survival strategy of nosocomial Staphylococcus haemolyticus. Microbiol Spectr 11:e0255222. (PMID: 36877037)

Marinho PF, Hanscheid T. 2023. A simple heat-based alternative method for deparaffinization of histological sections significantly improves acid-fast staining results for Mycobacteria in tissue. MethodsX 10:102079. (PMID: 36865652)

Schnyder JL, de Jong HK, Bache EB, van Hest RM, Schlagenhauf P, Borrmann S, Hanscheid T, Grobusch MP. 2023. On the potential for discontinuing atovaquone-proguanil (AP) ad-hoc post-exposure and other abbreviated AP-regimens: Pharmacology, pharmacokinetics and perspectives. Travel Med Infect Dis 52: In press (PMID: 36526126)

Mendes CI, Vila-Cerqueira P, Motro Y, Moran-Gilad J, Carriço JA, Ramirez M.. 2022. LMAS: evaluating metagenomic short de novo assembly methods through defined communities. Gigascience 12:giac122. (PMID: 36576131)

Kalkman LC, Hänscheid T, Krishna S, Grobusch MP. 2022. Fluid therapy in sepsis? Pathogen-specific perspectives. New Microbes New Infect 49–50:101035. (PMID: 36324876)

Kalkman LC, Hanscheid T, Krishna S, Kremsner PG, Grobusch MP. 2022. Antimalarial treatment in infants. Expert Opin Pharmacother 23:1711–1726. (PMID: 36174125)

Hernández-García M, García-Castillo M, 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. In vitro activity of imipenem/relebactam against Pseudomonas aeruginosa isolates recovered from ICU patients in Spain and Portugal (SUPERIOR and STEP studies). J Antimicrob Chemother 77:3163–3172. (PMID: 36059128)

Hernández-García M, García-Castillo M, Bou G, Cercenado E, Delgado-Valverde M, Oliver A, Pitart C, Rodríguez-Lozano J, Tormo N, 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. Imipenem-Relebactam Susceptibility in Enterobacterales Isolates Recovered from ICU Patients from Spain and Portugal (SUPERIOR and STEP Studies). Microbiol Spectr 10:e0292722. (PMID: 36043877)

Silva-Costa C, Gomes-Silva J, Pinho MD, Friães A, Ramirez M., Melo-Cristino J. 2022. Continued Vaccine Breakthrough Cases of Serotype 3 Complicated Pneumonia in Vaccinated Children, Portugal (2016-2019). Microbiol Spectr. 2022 Aug 31;10(4):e0107722.(PMID: 35862941)

Mukherjee D, Chora ÂF, Lone J-C, Ramiro RS, Blankenhaus B, Serre K, Ramirez M., Gordo I, Veldhoen M, Varga-Weisz P, Mota MM. 2022. lung microbiota promotes malaria-associated acute respiratory distress syndrome. Nat Commun 13:3747.(PMID: 35768411)

Schnyder JL, de Jong HK, Schlagenhauf P, Borrmann S, Hanscheid T, Grobusch MP. 2022. 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. Travel Med Infect Dis 49:102365. (PMID: 35661741)

Martins ER, Nascimento do Ó D, Marques Costa AL, Melo-Cristino J, Ramirez M. 2022. Characteristics of Streptococcus agalactiae colonizing nonpregnant adults support the opportunistic nature of invasive infections. Microbiol Spectr 10:e0108222. (PMID: 35604173)

Friães A, Mamede R, Ferreira M, Melo-Cristino J, Ramirez M. 2022. Annotated whole-genome multilocus sequence typing schema for scalable high-resolution typing of Streptococcus pyogenes. J Clin Microbiol 60:e0031522. (PMID: 35531659)

Elias R, Spadar A, Phelan J, Melo-Cristino J, Lito L, Pinto M, Gonçalves L, Campino S, Clark TG, Duarte A, Perdigão J. 2022. A phylogenomic approach for the analysis of colistin resistance-associated genes in Klebsiella pneumoniae, its mutational diversity and implications for phenotypic resistance. Int J Antimicrob Agents 59:106581.

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, Carriço JA, Scaturro M. 2022. Genome analysis of Legionella pneumophila ST23 from various countries reveals highly similar strains. Life Sci Alliance 5:e202101117. (PMID: 35236759)

Mendes G, Ramalho JF, Bruschy-Fonseca A, Lito L, Duarte A, Melo-Cristino J, Caneiras C. 2022. 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. Microorganisms 10:416. (PMID: 35208876)

Mendes G, Ramalho JF, Bruschy-Fonseca A, Lito L, Duarte A, Melo-Cristino J, Caneiras C. 2022. First Description of Ceftazidime/Avibactam Resistance in a ST13 KPC-70-Producing Klebsiella pneumoniae Strain from Portugal. Antibiotics (Basel) 11:167. (PMID: 35203770)

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. Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. Gigascience 11:giac003 (PMID: 35169842)

Kalkman LC, Hänscheid T, Krishna S, Grobusch MP. 2022. Fluid therapy for severe malaria. Lancet Infect Dis S1473-3099(21)00471–0. (PMID: 35051406)

Barros Pinto MP, Melo-Cristino J. 2021. Merozoites phagocytosed by neutrophils in Plasmodium falciparum malaria. Br J Haematol 196:9 (PMID: 34371526)

Pugliese CM, Adegbite BR, Edoa JR, Mombo-Ngoma G, Obone-Atome FA, Heuvelings CC, Bélard S, Kalkman LC, Leopold SJ, Hänscheid T, Adegnika AA, Huson MA, Grobusch MP. 2022. Point-of-care ultrasound to assess volume status and pulmonary oedema in malaria patients. Infection 50:65–82. (PMID: 34110570)

van der Putten BCL , Mendes CI, Talbot BM, de Korne-Elenbaas J, Mamede R, Vila-Cerqueira P, Coelho LP, Gulvik CA​, Katz LS​, The ASM NGS 2020 Hackathon participants. 2022. Software testing in microbial bioinformatics: a call to action. Microbial Genomics, Volume 8, Issue 3.(PMID: 35259087)

Elias R, Melo-Cristino J, Lito L, Pinto M, Gonçalves L, Campino S, Clark TG, Duarte A, Perdigão J. 2021. Klebsiella pneumoniae and colistin susceptibility testing: performance evaluation for broth microdilution, agar dilution and minimum inhibitory concentration test strips and impact of the “skipped well” phenomenon. Diagnostics 11:2352. (PMID: 34943590)

Adegbite BR, Edoa JR, Ndzebe Ndoumba WF, Dimessa Mbadinga LB, Mombo-Ngoma G, Jacob ST, Rylance J, Hänscheid T, Adegnika AA, Grobusch MP. 2021. A comparison of different scores for diagnosis and mortality prediction of adults with sepsis in Low-and-Middle-Income Countries: a systematic review and meta-analysis. EClinicalMedicine 42:101184. (PMID: 34765956)

Freitas AT, Calhau C, Antunes G, Araújo B, Bandeira M, Barreira S, Bazenga F, Braz S, Caldeira D, Santos SCR, Faria A, Faria D, Fraga M, Nogueira-Garcia B, Gonçalves L, Kovalchuk P, Lacerda L, Lopes H, Luís D, Medeiros F, Melo AMP, Melo-Cristino J, Miranda A, Pereira C, Pinto AT, Pinto J, Proença H, Ramos A, Rato JPR, Rocha F, Rocha JC, Moreira-Rosário A, Vazão H, Volovetska Y, Guimarães J-T, Pinto FJ. 2021. Vitamin D-related polymorphisms and vitamin D levels as risk biomarkers of COVID-19 disease severity. Sci Rep 11:20837. (PMID: 34675344)

Baeringsdottir B, Erlendsdottir H, Bjornsdottir ES, Martins ER, Ramirez M, Haraldsson A, Thorkelsson T. 2021. Group B streptococcal infections in infants in Iceland: clinical and microbiological factors. J Med Microbiol 70:001426 (PMID: 34554080)

Silva-Costa C, Gomes-Silva J, Prados L, Ramirez M, Melo-Cristino J, on behalf of the Portuguese Group for the Study of Streptococcal Infections, the Portuguese Study Group of Invasive Pneumococcal Disease of the Pediatric Infectious Disease Society. 2021. Pediatric invasive pneumococcal disease three years after PCV13 introduction in the national immunization plan - The continued importance of serotype 3. 7. Microorganisms 9:1428. (PMID: 34361864)

Hernández-García M, García-Fernández S, García-Castillo M, Pássaro L, Cantón R, STEP study group. 2021. In vitro characterization of Pseudomonas aeruginosa recovered in Portugal from low respiratory tract infections in ICU patients (STEP Study). FEMS Microbiol Lett 368:fnab099. (PMID: 34347078)

Grobusch MP, Schnyder J, Garcia-Garrido HM, Wisman JJ, Stijnis C, Goorhuis A, Hänscheid T, de Jong HK. 2021. Delayed large local reaction to the adenovirus-vectored (ChAdOx1) vaccine. Travel Med Infect Dis 43:102093. (PMID: 34102322)

Silva L, Queirós C, Borges-Costa J, Barreto R, Filipe P, Melo-Cristino J. 2021. Chlamydia trachomatis Infections in a Tertiary Care Portuguese Hospital: An 11-Year Retrospective Study. Actas Dermosifiliogr 112:528–533. (PMID: 34088478)

Silva-Costa C, Gomes-Silva J, Teodoro I, Ramirez M, Melo-Cristino J, on behalf of the Portuguese Group for the Study of Streptococcal Infections. 2021. Invasive Pneumococcal Disease in Adults in Portugal: The Importance of Serotypes 8 and 3 (2015–2018). 5. Microorganisms 9:1016. (PMID: 34066862)

Mäesaar M, Mamede R, Elias T, Roasto M. 2021. Retrospective Use of Whole-Genome Sequencing Expands the Multicountry Outbreak Cluster of Listeria monocytogenes ST1247. Int J Genomics 2021:6636138. (PMID: 33869622)

Grobusch MP, Hanscheid T. 2021. Dracunculiasis X in Vietnam: Emerging public health threat or exotic gem? Int J Infect Dis 105:416–417. (PMID: 33610782)

Mendes Pedro D, Mendes Pedro MM, Valadas E, Hanscheid T. 2021. SARS-CoV-2 and Cancer: Beyond Immunosuppression. Acta Med Port 34:237. (PMID: 33480839)

Hernández-García M, García-Fernández S, García-Castillo M, Melo-Cristino J, Pinto MF, Gonçalves E, Alves V, Costa E, Ramalheira E, Sancho L, Diogo J, Ferreira R, Silva T, Chaves C, Pássaro L, Paixão L, Romano J, Cantón R, STEP study group. 2021. Confronting ceftolozane-tazobactam susceptibility in multidrug-resistant Enterobacterales isolates and whole-genome sequencing results (STEP Study). Int J Antimicrob Agents 57:106259. (PMID: 33310115)

Hernández-García M, García-Castillo M, García-Fernández S, Melo-Cristino J, Pinto MF, Gonçalves E, Alves V, Vieira AR, Ramalheira E, Sancho L, Diogo J, Ferreira R, Silva T, Chaves C, Bou G, Cercenado E, Delgado-Valverde M, Oliver A, Pitart C, Rodríguez-Lozano J, Tormo N, Romano J, Pássaro L, Paixão L, López-Mendoza D, Díaz-Regañón J, Cantón R, STEP and SUPERIOR study groups. 2021. Distinct epidemiology and resistance mechanisms affecting ceftolozane/tazobactam in Pseudomonas aeruginosa isolates recovered from ICU patients in Spain and Portugal depicted by WGS. J Antimicrob Chemother 76:370–379. (PMID: 33099623)

Mamede R, Vila-Cerqueira P, Silva M, Carriço JA, Ramirez M. 2021. Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas. Nucleic Acids Res 49:D660–D666. (PMID: 33068420)

Queirós C, Borges da Costa J, Lito L, Filipe P, Melo-Cristino J. 2020. Gonorrhea in a tertiary care Portuguese hospital: a 10-year retrospective study of the evolution of cases and drug resistance of the isolates. Actas Dermosifiliogr 111:761–767. (PMID: 32997962)

Barros Pinto MP, Marques G, Melo-Cristino J. 2021 Promastigotes of Leishmania spp. developing in human bone marrow in vitro. Br J Haematol 192:7. (PMID: 32945533)

Vaz C, Nascimento M, Carriço JA, Rocher T, Francisco AP. 2020. Distance-based phylogenetic inference from typing data: a unifying view. Brief Bioinformatics 22:bbaa147. (PMID: 32734294)

Utzinger KS, Held U, Hänscheid T, Gültekin N, Fehr J, Grobusch MP, Schlagenhauf P. 2020. Self-diagnosis and self-treatment of Plasmodium spp. infection by travellers (1989-2019): A systematic review and meta-analysis. Travel Med Infect Dis 38:101902. (PMID: 33132136)

Figueiredo-Campos P, Blankenhaus B, Mota C, Gomes A, Serrano M, Ariotti S, Costa C, Nunes-Cabaço H, Mendes AM, Gaspar P, Pereira-Santos MC, Rodrigues F, Condeço J, Escoval MA, Santos M, Ramirez M, Melo-Cristino J, Simas JP, Vasconcelos E, Afonso Â, Veldhoen M. 2020. Seroprevalence of anti-SARS-CoV-2 antibodies in COVID-19 patients and healthy volunteers up to six months post disease onset. Eur J Immunol 50:2025–2040. (PMID: 33084029)

Dubbink JH, Branco TM, Kamara KB, Bangura JS, Wehrens E, Falama AM, Goorhuis A, Jørgensen PB, Sevalie SS, Hänscheid T, Grobusch MP. 2020. COVID-19 treatment in sub-Saharan Africa: If the best is not available, the available becomes the best. Travel Med Infect Dis 37:101878. (PMID: 32927051)

Pinto MPB, Melo-Cristino J. Sporogonic cycle of Plasmodium falciparum in a human blood. sample Am J Hematol In press. (PMID: 32857861)

Pinto M, Rodrigues JC, Matias R, Água-Doce I, Cordeiro D, Correia C, Gomes JP, Borrego MJ, PTGonoNet. 2020. Fifteen years of a nationwide culture collection of Neisseria gonorrhoeae antimicrobial resistance in Portugal. Eur J Clin Microbiol Infect Dis 39:1761–1770. (PMID: 32494956)

Grobusch MP, van der Fluit KS, Stijnis C, De Pijper CA, Hänscheid T, Gautret P, Schlagenhauf P, Goorhuis A. 2020. Can dengue virus be sexually transmitted? Travel Med Infect Dis 101753. (PMID: 32473313)

García-Fernández S, García-Castillo M, Melo-Cristino J, Pinto MF, Gonçalves E, Alves V, Vieira AR, Ramalheira E, Sancho L, Diogo J, Ferreira R, Silva D, Chaves C, Pássaro L, Paixão L, Cantón R, STEP Study Group. 2020. In vitro activity of ceftolozane-tazobactam against Enterobacterales and Pseudomonas aeruginosa causing urinary, intra-abdominal and lower respiratory tract infections in intensive care units in Portugal: The STEP multicenter study. Int J Antimicrob Agents 55:105887. (PMID: 31926283)

González-Díaz A, Machado MP, Càmara J, Yuste J, Varon E, Domenech M, Del Grosso M, Marimón JM, Cercenado E, Larrosa N, Quesada MD, Fontanals D, El-Mniai A, Cubero M, Carriço JA, Martí S, Ramirez M, Ardanuy C. 2020. Two multi-fragment recombination events resulted in the β-lactam-resistant serotype 11A-ST6521 related to Spain9V-ST156 pneumococcal clone spreading in south-western Europe, 2008 to 2016. Euro Surveill 25:pii=1900457.(PMID: 32347199)

Mendes CI,Lizarazo E, Machado MP, Silva DN, Tami A, Ramirez M, Couto N, Rossen JWA, Carriço JA. 2020. DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing. Microb Genom 6:e000328. (PMID: 32134380)

Hänscheid T, Valadas E, Grobusch MP. 2020. Coronavirus 2019-nCoV: Is the genie already out of the bottle? Travel Med Infect Dis 101577. (PMID: 32044388)

Hänscheid T, Vieira S, Ferreira P, Carvalho T, Belo S, Grobusch MP. 2020. The fluorescent acid-fast stain, auramine-O, stains schistosome eggs and may be an aid for detection. An old technique with a useful future? Travel Med Infect Dis 35:101569. (PMID: 32006658)

Xavier BB, Mysara M, Bolzan M, Ribeiro-Gonçalves B, Alako BTF, Harrison P, Lammens C, Kumar-Singh S, Goossens H, Carriço JA, Cochrane G, Malhotra-Kumar S. 2020. Bacpipe: a rapid, user-friendly whole-genome sequencing pipeline for clinical diagnostic bacteriology. iScience 23:100769. (PMID: 31887656)

van der Linden M, Mamede R, Levina N, Helwig P, Vila-Cerqueira P, Carriço JA, Melo-Cristino J, Ramirez M, Martins ER. 2020. Heterogeneity of penicillin-non-susceptible group B streptococci isolated from a single patient in Germany. J Antimicrob Chemother. 75:296–299. (PMID: 31740946)

Hänscheid T, Grobusch MP. 2020. Coenzyme Q10 and cerebral malaria in mice: Questionable interpretations, improbable usefulness in humans. Parasitol Int 74:101969. (PMID: 31421269)

Friães A, Melo-Cristino J, Ramirez M, Portuguese Group for the Study of Streptococcal Infections. 2019. Changes in emm types and superantigen gene content of Streptococcus pyogenes causing invasive infections in Portugal. Sci Rep 9:18051. (PMID: 31792274)

Hänscheid T, Schlagenhauf P, Grobusch MP. 2019. Atovaquone/proguanil for malaria chemoprophylaxis - Could a difference in susceptibility during hepatic development explain the need to continue drug intake for 7 days post-exposure? Travel Med Infect Dis 101527. (PMID: 31759143)

Duque-Valencia J, Forero-Muñoz NR, Díaz FJ, Martins E, Barato P, Ruiz-Saenz J. 2019. Phylogenetic evidence of the intercontinental circulation of a canine distemper virus lineage in the Americas. Sci Rep 9:15747. (PMID: 31673120)

Fleres G, Couto N, Schuele L, Chlebowicz M A, Mendes C I, van der Sluis L W M, Rossen J W A, Friedrich A W, García-Cobos S. 2019. Detection of a novel mcr-5.4 gene variant in hospital tap water by shotgun metagenomic sequencing. J Antimicrob Chemother 74: 3626–3628 (PMID: 31504580)

Espadinha D, Sobral R G, Mendes C I, Méric G, Sheppard S K, Carriço JA, de Lencastre H, Miragaia M. 2019. Distinct Phenotypic and Genomic Signatures Underlie Contrasting Pathogenic Potential of Staphylococcus epidermidis Clonal Lineages. Front Microbiol 10: 1971. (PMID: 31507574)

Dias O, Saraiva J, Faria C, Ramirez M, Pinto F, Rocha I. 2019. iDS372, a phenotypically reconciled model for the metabolism of Streptococcus pneumoniae strain R6. Front Microbiol 10:1283. (PMID: 31293525)

Barkham T, Zadoks RN, Azmai MNA, Baker S, Bich VTN, Chalker V, Chau ML, Dance D, Deepak RN, van Doorn HR, Gutierrez RA, Holmes MA, Huong LNP, Koh TH, Martins E, Mehershahi K, Newton P, Ng LC, Phuoc NN, Sangwichian O, Sawatwong P, Surin U, Tan TY, Tang WY, Thuy NV, Turner P, Vongsouvath M, Zhang D, Whistler T, Chen SL. 2019. One hypervirulent clone, sequence type 283, accounts for a large proportion of invasive Streptococcus agalactiae isolated from humans and diseased tilapia in Southeast Asia. PLoS Negl Trop Dis 13:e0007421. (PMID: 31246981)

Caneiras C, Lito L, Melo-Cristino J, Duarte A. 2019. Community- and hospital-acquired Klebsiella pneumoniae urinary tract infections in Portugal: virulence and antibiotic resistance. Microorganisms 7:138. doi:10.3390/microorganisms7050138

Pinho MD, Foster G, Pomba C, Machado MP, Baily JL, Kuiken T, Melo-Cristino J, Ramirez M, Portuguese Group for the Study of Streptococcal Infections. 2019. Streptococcus canis are a single population infecting multiple animal hosts despite the diversity of the universally present M-like protein SCM. Front Microbiol 10:631.doi:10.3389/fmicb.2019.00631 (PMID: 30984150)

Silva-Costa C, Brito MJ, Aguiar SI, Lopes JP, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Invasive Pneumococcal Disease of the Pediatric Infectious Disease Society. 2019. Dominance of vaccine serotypes in pediatric invasive pneumococcal infections in Portugal (2012-2015). Sci Rep 9:6. doi:10.1038/s41598-018-36799-x (PMID: 30626918)

Echániz-Aviles G, Guerreiro SI, Silva-Costa C, Mendes CI, Carriço JA, Carnalla-Barajas MN, Soto-Noguerón A, Velazquez-Meza ME, Melo-Cristino J, Luévanos-Velazquez A, Martínez-Medina L, Vázquez-Larios MDR, Ramirez M. 2019. Streptococcus pneumoniae serotype 3 in Mexico (1994-2017): decrease of the unusual CC4909 lineage post-PCV13 introduction. J Clin Microbiol. 57 e01354-18 doi:10.1128/JCM.01354-18 (PMID: 30404945)

Pinto M, González-Díaz A, Machado MP, Duarte S, Vieira L, Carriço JA, Marti S, Bajanca-Lavado MP, Gomes JP. 2019. Insights into the population structure and pan-genome of Haemophilus influenzae. Infect Genet Evol. 67:126–135 (PMID: 30391557)

Jesus TF, Ribeiro-Gonçalves B, Silva DN, Bortolaia V, Ramirez M, Carriço JA. 2019. Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data. Nucleic Acids Res 47:D188–D194 (PMID: 30395323)

Caneiras C, Lito L, Mayoralas-Alises S, Díaz-Lobato S, Melo-Cristino J, Duarte A. 2019. Virulence and resistance determinants of Klebsiella pneumoniae isolated from a Portuguese tertiary university hospital centre over a 31-year period. Enferm Infecc Microbiol Clin. 37:387–393. (PMID: 30553621)

Björnsdóttir ES, Martins ER, Erlendsdóttir H, Haraldsson G, Melo-Cristino J, Ramirez M, Kristinsson KG. 2019. Group B streptococcal neonatal and early infancy infections in Iceland 1976 - 2015. Pediatr Infect Dis J. 38:620–624. (PMID: 30299423)

Huizenga E, van der Ende J, Zwinkels N, Jimissa A, van der Ende-Bouwman C, van Rooijen R, Kargbo B, Agnandji ST, Hänscheid T, Goorhuis A, Grobusch MP. 2019. A modified case definition to facilitate essential hospital care during Ebola outbreaks. Clin Infect Dis. 68:1763–1768. (PMID: 30239602)

Hänscheid T, Grobusch MP. 2019. Could antibiotic treatment of traveller’s diarrhoea even prolong elimination of pathogens? Travel Med Infect Dis. 28:104. (PMID: 30030070)

Caneiras C, Calisto F, Jorge da Silva G, Lito L, Melo-Cristino J, Duarte A. 2018. First description of colistin and tigecycline-resistant Acinetobacter baumannii producing KPC-3 carbapenemase in Portugal. Antibiotics 7. doi:10.3390/antibiotics7040096 (PMID: 30404152)

Horácio AN, Silva-Costa C, Lopes E, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections. 2018. Conjugate vaccine serotypes persist as major causes of non-invasive pneumococcal pneumonia in Portugal despite declines in serotypes 3 and 19A (2012-2015). PLoS ONE 13:e0206912.doi:10.1371/journal.pone.0206912 (PMID: 30388168)

Hänscheid T, Hardisty DW, Henriques SO. 2018. The crisis in scientific publishing: a holistic perspective about background issues associated with predatory publishing. Acta Med Port 31:524–526. (PMID: 30387419)

Pato C, Melo-Cristino J, Ramirez M, Friães A, Portuguese Group for the Study of Streptococcal Infections. 2018. Streptococcus pyogenes causing skin and soft tissue infections are enriched in the recently emerged emm89 clade 3 and are not associated with abrogation of CovRS. Front Microbiol 9:2372.(PMID: 30356787)

Branco A, Melo-Cristino J. 2018. Extreme parasitemia in P. falciparum malaria. Blood 132:868. (PMID: 30139832)

Barreto JN, de Lourdes Monteiro M, da Luz Lima M, Valadas E, Hänscheid T. 2018. Under-reporting of tuberculosis in Praia, Cape Verde: study reports doubtful results. Int J Tuberc Lung Dis 22:1106. (PMID: 30092879)

Branco A, Francisco D, Hänscheid T. 2018. Is there a “normal” oxygen concentration for in vitro Plasmodium cultures? Trends Parasitol 34:811–812. (PMID: 30049603)

Couto N, Schuele L, Raangs EC, Machado MP, Mendes CI, Jesus TF, Chlebowicz M, Rosema S, Ramirez M,Carriço JA, Autenrieth IB, Friedrich AW, Peter S, Rossen JW. Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens. Sci Rep. 2018 Sep 13;8(1):13767. doi: 10.1038/s41598-018-31873-w.(PMID: 30213965)

Zhou Z, Alikhan NF, Sergeant MJ, Luhmann N, Vaz C, Francisco AP, Carriço JA, Achtman M. GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res. 2018 Sep;28(9):1395-1404. doi: 10.1101/gr.232397.117. Epub 2018 Jul 26. (PMID: 30049790)

Teixeira AS, Monteiro PT, Carriço JA, Santos FC, Francisco AP. 2018. Large-scale simulations of bacterial populations over complex networks. J Comput Biol 25:850–861. (PMID: 29985650)

Silva-Costa C, Brito MJ, Pinho MD, Friães A, Aguiar SI, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Invasive Pneumococcal Disease of the Pediatric Infectious Disease Society. 2018. Pediatric complicated pneumonia caused by Streptococcus pneumoniae serotype 3 in 13-valent pneumococcal conjugate vaccinees, Portugal, 2010-2015. Emerging Infect Dis 24: 1307–1314. (PMID: 29912700)

Grobusch MP, Schaumburg F, Weitzel T, Rothe C, Hänscheid T, Goorhuis A. 2018. Ebola 2018 - Implications for travel health advice and relevance for travel medicine. Travel Med Infect Dis 24:1–3. (PMID: 29906571)

Lopes E, Fernandes T, Machado MP, Carriço JA, Melo-Cristino J, Ramirez M, Martins ER, The Portuguese Group For The Study Of Streptococcal Infections. Increasing macrolide resistance among Streptococcus agalactiae causing invasive disease in non-pregnant adults was driven by a single capsular-transformed lineage, Portugal, 2009 to 2015. Euro Surveill. 2018;23. doi:10.2807/1560-7917.ES.2018.23.21.1700473 (PMID: 29845930)

Hänscheid T, Hardisty DW. 2018. How “resistant” is artemisinin resistant malaria? - The risks of ambiguity using the term “resistant” malaria. Travel Med Infect Dis 24:23–24. (PMID: 29715560)

Motro Y, Carriço JA, Friedrich AW, Rossen JW, Moran-Gilad J. 2018. ESCMID Postgraduate Education Course Regional Capacity Building for Integration of Next-Generation Sequencing in the Clinical Microlab. Microbes Infect 20:275–280. (PMID: 29555344)

Silva M, Machado MP, Silva DN, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço JA. 2018. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Microb Genom. 4. doi: 10.1099/mgen.0.000166. (PMID: 29543149)

Carriço JA, Crochemore M, Francisco AP, Pissis SP, Ribeiro-Gonçalves B, Vaz C. Fast phylogenetic inference from typing data. Algorithms Mol Biol. 2018 Feb 15;13:4. doi: 10.1186/s13015-017-0119-7. eCollection 2018. (PMID: 29467814)

Culebro A, Machado MP, Carriço JA, Rossi M. Origin, evolution, and distribution of the molecular machinery for biosynthesis of sialylated lipooligosaccharide structures in Campylobacter coli. Sci Rep. 2018 Feb 14;8(1):3028. doi: 10.1038/s41598-018-21438-2.(PMID: 29445215)

Carriço JA, Rossi M, Moran-Gilad J, Van Domselaar G, Ramirez M. 2018. A Primer on Microbial Bioinformatics for non-bioinformaticians. Clin Microbiol Infect. 24:342–349.(PMID: 29309933)

Savelkoel J, Binnendijk KH, Spijker R, van Vugt M, Tan K, Hänscheid T, Schlagenhauf P, Grobusch MP. 2018. Abbreviated atovaquone-proguanil prophylaxis regimens in travelers after leaving malaria-endemic areas: A systematic review. Travel Med Infect Dis. 21:3–20. (PMID: 29242073)

Hänscheid T, Grobusch MP. 2017. Modern hematology analyzers are very useful for diagnosis of malaria and, crucially, may help avoid misdiagnosis. J Clin Microbiol 55:3303–3304. (PMID: 29066565)

Guedes LC, Chan RB, Gomes MA, Conceição VA, Machado RB, Soares T, Xu Y, Gaspar P, Carriço JA, Alcalay RN, Ferreira JJ, Outeiro TF, Miltenberger-Miltenyi G. Serum lipid alterations in GBA-associated Parkinson's disease . Parkinsonism Relat Disord. 2017 Sep 1. pii: S1353-8020(17)30322-X. (PMID: 28890071)

Ribeiro TG, Ribeiro-Gonçalves B, da Silva MS, Novais A, Machado E, Carriço JA, Peixe L. Citrobacter portucalensis sp. nov., isolated from an aquatic sample . Int J Syst Evol Microbiol. 2017 Sep;67(9):3513-3517. (PMID: 28857032)

Jamet A, Touchon M, Ribeiro-Gonçalves B, Carriço JA, Charbit A, Nassif X, Ramirez M, Rocha EPC. 2017. A widespread family of polymorphic toxins encoded by temperate phages. BMC Biol 15:75. (PMID: 28851366)

Taboada EN, Graham MR, Carriço JA, Van Domselaar G. 2017. Food safety in the age of next generation sequencing, bioinformatics, and open data access. Front Microbiol 8:909. (PMID: 28588568)

Gil J, Almeida S, Constant C, Pinto S, Barreto R, Melo-Cristino J, Machado M do C, Bandeira T. 2017. Short-term relevance of lower respiratory viral coinfection in inpatients under 2 years of age. An Pediatr In press (PMID: 28571896)

Visser BJ, de Vries SG, Vingerling R, Gritter M, Kroon D, Aguilar LC, Kraan RBJ, Wieten RW, Danion F, Sjouke B, Adegnika AA, Agnandji ST, Kremsner PG, Hänscheid T, Mens PF, van Vugt M, Grobusch MP. 2017. Serum lipids and lipoproteins during uncomplicated malaria: A cohort study in Lambaréné, Gabon. Am J Trop Med Hyg 96:1205–1214. (PMID: 28500816)

Martins ER, Pedroso-Roussado C, Melo-Cristino J, Ramirez M, Portuguese Group for the Study of Streptococcal Infections. 2017. Streptococcus agalactiae causing neonatal infections in Portugal (2005-2015): diversification and emergence of a CC17/PI-2b multidrug resistant sublineage. Front Microbiol 8:499. (PMID: 28400757)

Marchaim D, Levit D, Zigron R, Gordon M, Lazarovitch T, Carriço JA, Chalifa-Caspi V, Moran-Gilad J. 2017. Clinical and molecular epidemiology of Acinetobacter baumannii bloodstream infections in an endemic setting. Future Microbiol 12:271–283. (PMID: 28287300)

Henriques AR, Melo-Cristino J, Fraqueza MJ. 2017. Genetic characterization of Listeria monocytogenes isolates from industrial and retail ready-to-eat meat-based foods and their relationship with clinical strains from human listeriosis in Portugal. J Food Prot 551–560. (PMID: 28272920)

Diamantino-Miranda J, Aguiar, SI, Carriço JA, Melo-Cristino J, Ramirez M. 2017. Clonal and serotype dynamics of serogroup 6 isolates causing invasive pneumococcal disease in Portugal: 1999-2012. PLoS ONE 12:e0170354. (PMID: 28152029)

Machado MP, Ribeiro-Gonçalves B, Silva M, Ramirez M, Carriço JA. 2017. Epidemiological surveillance and typing methods to track antibiotic resistant strains using high throughput sequencing. Methods Mol Biol 1520:331–355. (PMID: 27873262)

Nascimento M, Sousa A, Ramirez M, Francisco AP, Carriço JA, Vaz C. 2017. PHYLOViZ 2.0: Providing scalable data integration and visualization for multiple phylogenetic inference methods. Bioinformatics 33:128–129. (PMID: 27605102)

Horácio AN, Silva-Costa C, Lopes JP, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections. 2016. Serotype 3 remains the leading cause of invasive pneumococcal disease in adults in Portugal (2012-2014) despite continued reductions in other 13-valent conjugate vaccine serotypes. Front Microbiol 7:1616. (PMID: 27790208)

Barato P, Martins ER, Vasquez GM, Ramirez M, Melo-Cristino J, Martínez N, Iregui C. 2016. Capsule impairs efficient adherence of Streptococcus agalactiae to intestinal epithelium in tilapias Oreochromis sp. Microb Pathog. 100:30–36. (PMID: 27594667)

Pinho MD, Erol E, Ribeiro-Gonçalves B, Mendes CI, Carriço JA, Matos SC, Preziuso S, Luebke-Becker A, Wieler LH, Melo-Cristino J, Ramirez M. 2016. Beta-hemolytic Streptococcus dysgalactiae strains isolated from horses are a genetically distinct population within the Streptococcus dysgalactiae taxon. Sci Rep 6:31736. (PMID: 27530432)

Costa SS, Palma C, Kadlec K, Fessler AT, Viveiros M, Melo-Cristino J, Schwarz S, Couto I. 2016. Plasmid-borne antimicrobial resistance of Staphylococcus aureus isolated in a hospital in Lisbon, Portugal. Microb Drug Resist. 22:617–626. (PMID: 27309487)

Mottola C, Matias CS, Mendes JJ, Melo-Cristino J, Tavares L, Cavaco-Silva P, Oliveira M. 2016. Susceptibility patterns of Staphylococcus aureus biofilms in diabetic foot infections. BMC Microbiol 16:119.(PMID: 27339028)

Horácio AN, Silva-Costa C, Diamantino-Miranda J, Lopes JP, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections. 2016. Population structure of Streptococcus pneumoniae causing invasive disease in adults in Portugal before PCV13 availability for adults: 2008-2011. PLoS ONE 11:e0153602. (PMID: 27168156)

Ribeiro-Gonçalves B, Francisco AP, Vaz C, Ramirez M, Carriço JA. 2016. PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees. Nucleic Acids Res. 44:W246-251. (PMID: 27131357)

Vieira S, Belo S, Hänscheid T. 2016. Ziehl-Neelsen in schistosomiasis:much more than staining the shell and species identification. Am J Trop Med Hyg 94:699–700. (PMID: 27053189)

Rebelo M, Hänscheid T. 2016. Flow Cytometry for Antimalarial Drug Testing: More than Meets the Eye. J Clin Microbiol 54:817. (PMID: 26917459)

Mottola C, Semedo-Lemsaddek T, Mendes JJ, Melo-Cristino J, Tavares L, Cavaco-Silva P, Oliveira M. 2016. Molecular typing, virulence traits and antimicrobial resistance of diabetic foot staphylococci. J Biomed Sci 23:33. (PMID: 26952716)

Rebelo M, Grenho R, Orban A, Hänscheid T. 2016. Transdermal diagnosis of malaria using vapor nanobubbles. Emerging Infect Dis 22:343–344. (PMID: 26811926)

Hänscheid T, Carvalho T, Grobusch MP. 2016. Hemozoin detection for human malaria diagnosis investigated in rodent models: how similar is similar? Trends Parasitol. 32: 94–96 (PMID: 26704075)

Pires D, Zagalo A, Santos C, Cota de Medeiros F, Duarte A, Lito L, Melo-Cristino J, Caldeira L. 2016. Evolving epidemiology of carbapenemase-producing Enterobacteriaceae in Portugal: 2012 retrospective cohort at a tertiary hospital in Lisbon. J Hosp Infect 92:82–85. (PMID: 26698390)

Björnsdóttir ES, Martins ER, Erlendsdóttir H, Haraldsson G, Melo-Cristino J, Kristinsson KG, Ramirez M. 2016. Changing epidemiology of group B streptococcal infections among adults in Iceland: 1975-2014. Clin Microbiol Infect. 22:379.e9-379.e16. (PMID: 26691681)

Friães A, Machado MP, Pato C, Carriço JA, Melo-Cristino J, Ramirez M. 2015. Emergence of the same successful clade among distinct populations of emm89 Streptococcus pyogenes in multiple geographic regions. MBio 6. pii: e01780-15. (PMID: 26628724) (Highlighted in Holzman DC. 2016. To outcompete others, S. pyogenes clade undergoes transmissibility upgrade. Microbe 11:56-57)

Costa SS, Viveiros M, Rosato AE, Melo-Cristino J, Couto I. 2015. Impact of efflux in the development of multidrug resistance phenotypes in Staphylococcus aureus. BMC Microbiol 15:232.(PMID: 26498754)

Tempera C, Franco R, Caro C, André V, Eaton P, Burke P, Hänscheid T. 2015. Characterization and optimization of the haemozoin-like crystal (HLC) assay to determine Hz inhibiting effects of anti-malarial compounds. Malar J 14:403. (PMID: 26458401)

Barreira R, Graça AM, Gonçalves C, Abrantes M, Gouveia R, Carvalho D, Lito L, Moniz C, Melo-Cristino J, Machado MC. 2015. Monitorização epidemiológica numa unidade de cuidados intensivos neonatais. Acta Pediátrica Portuguesa 46:190–7. Publisher

Arinto-Garcia R, Pinho MD, Carriço JA, Melo-Cristino J, Ramirez M. 2015. Comparing MALDI-TOF MS, phenotypic and molecular methods for the identification of species within the Streptococcus anginosus group. J Clin Microbiol. 53:3580–3588. (PMID: 26354817)

Friães A, Pato C, Melo-Cristino J, Ramirez M. 2015. Consequences of the variability of the CovRS and RopB regulators among Streptococcus pyogenes causing human infections. Sci Rep 5:12057. (PMID: 26174161)

Silva-Costa C, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections. 2015. Declining macrolide resistance in Streptococcus pyogenes in Portugal (2007-13) was accompanied by continuous clonal changes. J Antimicrob Chemother. 70:2729–2733. (PMID: 26142474)

Coutinho CP, Barreto C, Pereira L, Lito L, Melo-Cristino J, Sá-Correia I. 2015. Incidence of Burkholderia contaminans at a cystic fibrosis centre with an unusually high representation of Burkholderia cepacia during 15 years of epidemiological surveillance. J Med Microbiol 64:927–935. (PMID: 26002942)

Ramirez M, Carriço JA, van der Linden M, Melo-Cristino J. 2015. Molecular Epidemiology of Streptococcus pneumoniae, p. 3-19 . In Brown, JM, Hammerschmidt, S, Orihuela, C (eds.), Streptococcus Pneumoniae - Molecular Mechanisms of Host-Pathogen Interactions. Academic Press, San Diego. DOI: 10.1016/B978-0-12-410530-0.00001-6

Janssen S, Hermans S, Knap M, Moekotte A, Rossatanga EG, Adegnika AA, Bélard S, Hänscheid T, Grobusch MP. 2015. Impact of Anti-Retroviral Treatment and Cotrimoxazole Prophylaxis on Helminth Infections in HIV-Infected Patients in Lambaréné, Gabon. PLoS Negl Trop Dis 9:e0003769. (PMID: 25993501)

Rosini R, Campisi E, De Chiara M, Tettelin H, Rinaudo D, Toniolo C, Metruccio M, Guidotti S, Sørensen UBS, Kilian M, DEVANI Consortium, Ramirez M, Janulczyk R, Donati C, Grandi G, Margarit I. 2015. Genomic analysis reveals the molecular basis for capsule loss in the group B streptococcus population. PLoS ONE 10:e0125985. (PMID: 25946017)

Rebelo M, Tempera C, Fernandes JF, Grobusch MP, Hänscheid T. 2015. Assessing anti-malarial drug effects ex vivo using the haemozoin detection assay. Malar J 14:140. (PMID: 25879757)

Rebelo M, Tempera C, Bispo C, Andrade C, Gardner R, Shapiro HM, Hänscheid T. 2015. Light depolarization measurements in malaria: A new job for an old friend. Cytometry A 87:437–445. (PMID: 25808846)

Teixeira AS, Monteiro PT, Carriço JA, Ramirez M, Francisco AP. 2015. Not seeing the forest for the trees: Size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis. PLoS ONE 10:e0119315. (PMID: 25799056)

Coelho LP, Pato C, Friães A., Neumann A, von Köckritz-Blickwede M, Ramirez M, Carriço JA. 2015. Automatic Determination of NET (Neutrophil Extracellular Traps) Coverage in Fluorescent Microscopy Images. Bioinformatics 31:2364–2370. (PMID: 25792554)

Silva-Costa C, Friães A, Ramirez M, Melo-Cristino J 2015. Macrolide-resistant Streptococcus pyogenes: prevalence and treatment strategies. Expert Rev Anti Infect Ther 13:615–628. (PMID: 25746210)

Barato P, Martins ER, Melo-Cristino J, Iregui CA, Ramirez M. 2015. Persistence of a single clone of Streptococcus agalactiae causing disease in tilapia (Oreochromis sp.) cultured in Colombia over 8 years. J Fish Dis 38:1083–1087 (PMID: 25643734)

Friães A, C. Resina, V. Manuel, L. Lito, Ramirez M, and Melo-Cristino J. 2015. Epidemiological survey of the first case of vancomycin-resistant Staphylococcus aureus infection in Europe. Epidemiol Infect 143:745–8. (PMID: 24901752)

Vaz C, Francisco AP, Silva M, Jolley KA, Bray JE, Pouseele H, Rothganger J, Ramirez M, Carriço JA. 2014. TypOn: the microbial typing ontology. J Biomed Semantics 5:43. (PMID: 25584183)

Magalhães R, Ferreira V, Santos I, Almeida G, Teixeira P, Research Team. 2014. Genetic and phenotypic characterization of Listeria monocytogenes from human clinical cases that occurred in Portugal between 2008 and 2012. Foodborne Pathog. Dis. 11:907–916. (PMID: 25361468)

Earnshaw S, Mancarella G, Mendez A, Todorova B, Magiorakos AP, Possenti E, Stryk M, Gilbro S, Goossens H, Albiger B, Monnet DL, European Antibiotic Awareness Day Technical Advisory Committee, European Antibiotic Awareness Day Collaborative Group. 2014. European Antibiotic Awareness Day: a five-year perspective of Europe-wide actions to promote prudent use of antibiotics. Euro Surveill. 19: pii: 20928. (PMID: 25345519)

Ramirez M. 2014. Streptococcus pneumoniae, p. 1529–1546. In Tang, Y-W, Sussman, M, Liu, D, Poxton, I, Schwartzman, J (eds.), Molecular Medical Microbiology, 2nd ed. Academic Press, Elsevier. (DOI: 10.1016/B978-0-12-397169-2.00086-X)

Hänscheid T, Rebelo M, Grobusch MP. 2014. Point-of-care tests: where is the point? Lancet Infect Dis 14:922. (PMID: 25253406)

Carriço JA, Ramirez M. 2014. Analysis of typing results, p. 85–112. In Oyarzabal, OA, Kathariou, S (eds.), DNA Methods in Food Safety: Molecular Typing of Foodborne and Waterborne Bacterial Pathogens. John Wiley & Sons, Ltd. (DOI: 10.1002/9781118278666.ch5)

Branquinho R, Meirinhos-Soares L, Carriço JA, Pintado M, Peixe LV. 2014 Phylogenetic and clonality analysis of Bacillus pumilus isolates uncovered a highly heterogeneous population of different closely related species and clones. FEMS Microbiol Ecol. 2014 90:689–698. (PMID: 25230950)

Branquinho R, Sousa C, Osório H, Meirinhos-Soares L, Lopes J, Carriço J, Busse H-J, Abdulmawjood A, Klein G, Kämpfer P, Pintado ME, Peixe L. 2014. Bacillus invictae sp. nov., isolated from health products in Portugal. Int. J. Syst. Evol. Microbiol. 64:3867–3876. (PMID: 25171924)

Neumann A, Völlger L, Berends ETM, Molhoek EM, Stapels DAC, Midon M, Friães A, Pingoud A, Rooijakkers SHM, Gallo RL, Mörgelin M, Nizet V, Naim HY, von Köckritz-Blickwede M. 2014. Novel role of the antimicrobial peptide LL-37 in the protection of neutrophil extracellular traps against degradation by bacterial nucleases. J Innate Immun 6:860–868. (PMID: 25012862)

Horácio, AN, Lopes JP, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections. 2014. Non-invasive pneumococcal pneumonia in Portugal - serotype distribution and antimicrobial resistance. PLoS ONE 9:e103092. (PMID: 25075961)

Hänscheid T, Gresnigt T, Löhr S, Flamen A, Zoller T, Melo-Cristino J, Grobusch MP. 2014. Methaemoglobin and COHb in patients with malaria. Malar. J. 13:285. (PMID: 25056571)

Mendes JJ, Leandro C, Mottola C, Barbosa R, Silva FA, Oliveira M, Vilela CL, Melo-Cristino J, Górski A, Pimentel M, São-José C, Cavaco-Silva P, Garcia M. 2014. In vitro design of a novel lytic bacteriophage cocktail with therapeutic potential against organisms causing diabetic foot infections. J. Med. Microbiol. 63:1055–1065. (PMID: 24869663)

Orbán, A., Á. Butykai, A. Molnár, Z. Pröhle, G. Fülöp, T. Zelles, W. Forsyth, D. Hill, I. Müller, L. Schofield, M. Rebelo, T. Hänscheid, S. Karl, and I. Kézsmárki. 2014. Evaluation of a novel magneto-optical method for the detection of malaria parasites. PLoS ONE 9:e96981. (PMID: 24824542)

Olafsdottir, L., H. Erlendsdottir, J. Melo-Cristino, D. Weinberger, M. Ramirez, K. Kristinsson, and M. Gottfredsson. 2014. Invasive infections due to Streptococcus pyogenes: seasonal variation of severity and clinical characteristics, Iceland, 1975 to 2012. Euro Surveill. 19:pii: 20784 (PMID: 24821122)

Carrasco, M. P., A. S. Newton, L. Gonçalves, A. Góis, M. Machado, J. Gut, F. Nogueira, T. Hänscheid, R. C. Guedes, D. J. V. A. Dos Santos, P. J. Rosenthal, and R. Moreira. 2014. Probing the aurone scaffold against Plasmodium falciparum: Design, synthesis and antimalarial activity. Eur J Med Chem 80:523–534. (PMID: 24813880)

Preziuso, S., M. D. Pinho, A. R. Attili, J. Melo-Cristino, E. Acke, A. C. Midwinter, V. Cuteri, and M. Ramirez. 2014. PCR based differentiation between Streptococcus dysgalactiae subsp. equisimilis strains isolated from humans and horses. Comp. Immunol. Microbiol. Infect. Dis. 37(3): 169-72. (PMID: 24813401)

Sanderson-Smith M, De Oliveira DMP, Guglielmini J, McMillan DJ, Vu T, Holien JK, Henningham A, Steer AC, Bessen DE, Dale JB, Curtis N, Beall BW, Walker MJ, Parker MW, Carapetis JR, Van Melderen L, Sriprakash KS, Smeesters PR, The M Protein Study Group. 2014. A systematic and functional classification of Streptococcus pyogenes that serves as a new tool for molecular typing and vaccine development. J Infect Dis 210:1325–1338. (PMID: 24799598)

López, E., A. Domenech, M.-J. Ferrándiz, M. J. Frias, C. Ardanuy, M. Ramirez, E. García, J. Liñares, and A. G. de la Campa. 2014. Induction of prophages by fluoroquinolones in Streptococcus pneumoniae: implications for emergence of resistance in genetically-related clones. PLoS ONE 9:e94358. (PMID: 24718595)

Aguiar, SI, Brito M, Horácio, AN, Lopes J, Ramirez M, Melo-Cristino J, and Portuguese Group for the Study of Streptococcal Infections and the Portuguese Study Group of Invasive Pneumococcal Disease of the Paediatric Infectious Disease Society. 2014. Decreasing incidence and changes in serotype distribution of invasive pneumococcal disease in persons aged under 18 years since introduction of 10-valent and 13-valent conjugate vaccines in Portugal, July 2008 to June 2012. Euro Surveill. 19:pii: 20750. (PMID: 24698140)

Carrolo, M, Pinto FR, Melo-Cristino J, and Ramirez M. 2014. Pherotype influences biofilm growth and recombination in Streptococcus pneumoniae. PLoS ONE 9:e92138. (PMID: 24646937)

Cardoso, L. S., C. E. Suissas, M. Ramirez, M. Antunes, and F. R. Pinto. 2014. Comparison of alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays. BMC Res Notes 7:148.(PMID: 24629208)

Moreira, A. S., C. P. Coutinho, P. Avezedo, L. Lito, J. Melo-Cristino, and I. Sá-Correia. 2014. Burkholderia dolosa phenotypic variation during the decline in lung function of a cystic fibrosis patient along 5.5 years of chronic colonization. J. Med. Microbiol. 63:594–601. (PMID: 24469681)

Silva-Costa, C. , J. A. Carriço, M. Ramirez, and J. Melo-Cristino. 2014. Scarlet fever is caused by a limited number of Streptococcus pyogenes lineages and is associated with the exotoxin genes ssa, speA and speC. Pediatr Infect Dis J. 33(3):306-10. (PMID: 24168973)

Bajanca-Lavado MP, Simões AS, Betencourt CR, Sá-Leão R, Portuguese Group for Study of Haemophilus influenzae invasive infection. 2014. Characteristics of Haemophilus influenzae invasive isolates from Portugal following routine childhood vaccination against H. influenzae serotype b (2002-2010). Eur J Clin Microbiol Infect Dis 33:603–610. (PMID: 24154654)

Costa, A., J. Afonso, C. Osório, A. L. Gomes, F. Caiado, J. Valente, S. I. Aguiar, F. Pinto, M. Ramirez, S. Dias. 2013. miR-363-5p regulates endothelial cell properties and their communication with hematopoietic precursor cells. J Hematol Oncol 6:87. (PMID: 24257019)

Faria, N. A., M. Miragaia, and H. de Lencastre, and the Multi Laboratory Project Collaborators. 2013. Massive dissemination of methicillin resistant Staphylococcus aureus in bloodstream infections in a high mrsa prevalence country: establishment and diversification of EMRSA-15. Microb. Drug Resist. 19:483–490. (PMID: 24171450)

Horácio, A. N., J. Diamantino-Miranda, S. I. Aguiar, M. Ramirez, J. Melo-Cristino, and the Portuguese Group for the Study of Streptococcal Infections. 2013. The majority of adult pneumococcal invasive infections in Portugal are still potentially vaccine preventable in spite of significant declines of serotypes 1 and 5. PLoS ONE 8:e73704. (PMID: 24066064)

Ressurreição, A. S., D. Gonçalves, A. R. Sitoe, I. S. Albuquerque, J. Gut, A. Góis, L. M. Gonçalves, M. R. Bronze, T. Hänscheid, G. A. Biagini, P. J. Rosenthal, M. Prudêncio, P. O’Neill, M. M. Mota, F. Lopes, and R. Moreira. 2013. Structural optimization of Quinolon-4(1H)-imines as dual-stage antimalarials: toward increased potency and metabolic stability. J Med Chem. 56:7679–7690. (PMID: 23499920)

Boura, M., R. Frita, A. Góis, T. Carvalho, and T. Hänscheid. 2013. The hemozoin conundrum: is malaria pigment immune-activating, inhibiting, or simply a bystander? Trends Parasitol. 29:469–476. (PMID: 23937890)

Friães A., Lopes J.P., Melo-Cristino J., M. Ramirez, the Portuguese Group for the Study of Streptococcal Infections. 2013. Changes in Streptococcus pyogenes causing invasive disease in Portugal: Evidence for superantigen gene loss and acquisition. Int J Med Microbiol. 303:505-513 (PMID: 23932912)

Costa, S. S., E. Junqueira, C. Palma, M. Viveiros, Melo-Cristino J. , L. Amaral, I. Couto. 2013. Resistance to antimicrobials mediated by efflux pumps in Staphylococcus aureus. Antibiotics 2: 83-99, 2013. (doi:10.3390/antibiotics2010083)

Hanson, K. K., A. S. Ressurreição, K. Buchholz, M. Prudêncio, J. D. Herman-Ornelas, M. Rebelo, W. L. Beatty, D. F. Wirth, T. Hänscheid, R. Moreira, M. Marti, and M. M. Mota. 2013. Torins are potent antimalarials that block replenishment of Plasmodium liver stage parasitophorous vacuole membrane proteins. Proc Natl Acad Sci USA. 110:E2838–2847. (PMID: 23836641)

Shapiro, H. M., S. H. Apte, G. M. Chojnowski, T. Hänscheid, M. Rebelo, and B. T. Grimberg. 2013. Cytometry in malaria–a practical replacement for microscopy? Curr Protoc Cytom Chapter 11:Unit 11.20. (PMID: 23835802)

Melo-Cristino J., C. Resina, V. Manuel, L. Lito, M. Ramirez. 2013. First case of infection with vancomycin-resistant Staphylococcus aureus in Europe. The Lancet. 382:205 (PMID: 23791472)

Mendes J.J., C. Leandro, S. Corte-Real, R. Barbosa, P. Cavaco-Silva, J. Melo-Cristino, A. Górski, M. Garcia. 2013. Wound healing potential of topical bacteriophage therapy on diabetic cutaneous wounds. Wound Repair Regen. 21:595-603. (PMID: 23755910)

Rebelo, M., C. Sousa, H. M. Shapiro, M. M. Mota, M. P. Grobusch, and T. Hänscheid. 2013. A novel flow cytometric hemozoin detection assay for real-time sensitivity testing of Plasmodium falciparum. PLoS ONE 8:e61606. (PMID: 23637865)

Tavares, A., M. Miragaia, J. Rolo, C. Coelho, H. de Lencastre, and CA-MRSA/MSSA working group. 2013. High prevalence of hospital-associated methicillin-resistant Staphylococcus aureus in the community in Portugal: evidence for the blurring of community-hospital boundaries. Eur. J. Clin. Microbiol. Infect. Dis. 32:1269–1283. (PMID: 23604782)

Espadinha, D., N. A. Faria, M. Miragaia, L. M. Lito, J. Melo-Cristino, and H. de Lencastre. 2013. Extensive dissemination of methicillin-resistant Staphylococcus aureus (MRSA) between the hospital and the community in a country with a high prevalence of nosocomial MRSA. PLoS ONE 8:e59960. (PMID: 23593155)

Gouveia, C., A. Friães, M. Cassiano-Neves, J. Melo-Cristino, and M. Ramirez. 2013. MRSA and PVL positive Staphylococcus aureus are rarely found in community-acquired osteoarticular infections in children in Portugal, a country with high MRSA prevalence. Online Int J of Micr Res 1:20–24. (Online)

Vaz, M., L. Meirinhos-Soares, C. C. S. Sousa, M. Ramirez, J. Melo-Cristino, J. A. Lopes. 2013. Serotype discrimination of encapsulated Streptococcus pneumoniae strains by Fourier-transform infrared spectroscopy and chemometrics. J. Microbiol. Methods 93:102–107. (PMID: 23499920)

Valadas, E., A. Gomes, A. Sutre, S. Brilha, A. Wete, T. Hänscheid, and F. Antunes. 2013. Tuberculosis with malaria or HIV co-infection in a large hospital in Luanda, Angola. J Infect Dev Ctries 7:269–272. (PMID: 23493006)

McMillan, D. J., P.-A. Drèze, T. Vu, D. E. Bessen, J. Guglielmini, A. C. Steer, J. R. Carapetis, L. Van Melderen, K. S. Sriprakash, P. R. Smeesters and the M protein study group. 2013. Updated model of group A Streptococcus M proteins based on a comprehensive worldwide study. Clin. Microbiol. Infect. 19:E222–229. (PMID: 23464795)

Costa, S. S., C. Mourato, M. Viveiros, J. Melo-Cristino, L. Amaral, and I. Couto. 2013. Description of plasmid pSM52, harbouring the gene for the Smr efflux pump, and its involvement in resistance to biocides in a meticillin-resistant Staphylococcus aureus strain. Int. J. Antimicrob. Agents. 41:490–492. (PMID: 23434536)

Coelho JR, Carriço JA, Knight D, Martínez JL, Morrissey I, Oggioni MR, Freitas AT. 2013 The use of machine learning methodologies to analyse antibiotic and biocide susceptibility in Staphylococcus aureus. PLoS One. 2013;8(2):e55582. doi: 10.1371/journal.pone.0055582. Epub 2013 Feb 19. (PMID: 23431361)

J. A. Carriço, A. Sabat , A. Friederich, M. Ramirez, on behalf of the ESCMID Study Group for Epidemiological Markers (ESGEM). 2013. Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution. Euro Surveill. 2013. 18:pii=20382. (PMID: 23369390)

Pinho M. D., S. C. Matos, C. Pomba, A. Lübke-Becker, L. H. Wieler, S. Preziuso, J. Melo-Cristino, M. Ramirez. 2013. Multilocus sequence analysis of Streptococcus canis confirms the zoonotic origin of human infections and reveals genetic exchange with Streptococcus dysgalactiae subsp. equisimilis. J. Clin. Microbiol. 51:1099-109. (PMID: 23345291)

Martins E. R., A. Andreu, J. Melo-Cristino, and M. Ramirez. 2013. Distribution of pilus islands in Streptococcus agalactiae causing human infections: insights into evolution and implication for vaccine development. Clin. Vaccine Immunol. 20:313–316. (PMID: 23269415)

Janssen, S., X. Padanilam, R. Louw, R. Mahanyele, G. Coetzee, T. Hänscheid, T. Leenstra, and M. P. Grobusch. 2013. Sputum culture results to monitor MDR-TB patients during treatment: How many do we need? J. Clin. Microbiol. 51:644-6. (PMID: 23224098)

Frias, M. J., J. Melo-Cristino, M. Ramirez. 2013. Export of the pneumococcal phage SV1 lysin requires choline-containing teichoic acids and is holin-independent. Mol Microbiol. 87:430–445. (PMID: 23171061)

A. Friães, Pinto FR, C. Silva-Costa, M. Ramirez, J. Melo-Cristino 2013. Superantigen gene complement of Streptococcus pyogenes - relationship with other typing methods and short-term stability. Eur. J. Clin. Microbiol. Infect. Dis. 32:115-125. (PMID: 22936424)

A. Friães, Pinto FR, C. Silva-Costa, M. Ramirez, J. Melo-Cristino, The Portuguese Group for the Study of Streptococcal Infections. 2012. Group A streptococci clones associated with invasive infections and pharyngitis in Portugal present differences in emm types, superantigen gene content and antimicrobial resistance. BMC Microbiol. 12:280.(PMID: 23181337)

C. Silva-Costa, A. Friães, M. Ramirez, J. Melo-Cristino, The Portuguese Group for the Study of Streptococcal Infections. 2012. Differences between macrolide resistant and susceptible Streptococcus pyogenes: the importance of clonal properties in addition to antibiotic consumption. Antimicrob Agents Chemother. 56:5661–5666. (PMID: 22908153)

Thomas, V., A. Góis, B. Ritts, P. Burke, T. Hänscheid, and G. McDonnell. 2012. A novel way to grow hemozoin-like crystals in vitro and its use to screen for hemozoin inhibiting antimalarial compounds. PLoS ONE 7:e41006. (PMID: 22815894)

Portuguese Laboratory Network for the Diagnosis of Influenza Infection. 2012. Contribution of the Portuguese Laboratory Network for the Diagnosis of Influenza A(H1N1)pdm09 infection during the 2009/10 and 2010/11 influenza seasons. Euro Surveill. 17. (PMID: 22790607)

S. I. Aguiar, J. Melo-Cristino, and M. Ramirez. 2012. Use of the 13-valent conjugate vaccine has the potential to eliminate pilus carrying isolates as causes of invasive pneumococcal disease. Vaccine 30:5487–5490. (PMID: 22749798)

Francisco, A.P., C. Vaz, P. T. Monteiro, J. Melo-Cristino, M. Ramirez, and J. A. Carriço. 2012. PHYLOViZ: Phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics, 13:87 (PMID: 22568821)

Frita, R., D. Carapau, M. M. Mota, and T. Hänscheid. 2012. In vivo hemozoin kinetics after clearance of Plasmodium berghei infection in mice. Malar Res Treat 2012:373086. (PMID: 22567535)

Almeida, J., J. Tiple, M. Ramirez, J. Melo-Cristino, C. Vaz, A. P. Francisco, and J. A. Carriço. 2012. An Ontology and a REST API for Sequence Based Microbial Typing Data, p. 21–28. In A.T. Freitas, and A. Navarro (eds.), Bioinformatics for Personalized Medicine. Springer Berlin Heidelberg, Berlin, Heidelberg. DOI: 10.1007/978-3-642-28062-7_3

Rebelo, M., H. M. Shapiro, T. Amaral, J. Melo-Cristino, and T. Hänscheid. 2012. Haemozoin detection in infected erythrocytes for Plasmodium falciparum malaria diagnosis-Prospects and limitations. Acta Tropica. 123:58-61. (PMID: 22465900)

Martins E. R., J. Melo-Cristino, M. Ramirez, Portuguese Group for the Study of Streptococcal Infections. 2012. Dominance of serotype Ia among group B streptococci causing invasive infections in non-pregnant adults in Portugal. J Clin Microbiol. 50:1219–1227. (PMID: 22219307)

Horácio, A. N., J. Diamantino-Miranda, S. I. Aguiar, M. Ramirez, J. Melo-Cristino and the Portuguese Group for the Study of Streptococcal Infections. 2012. Serotype changes in adult invasive pneumococcal infections in Portugal did not reduce the high fraction of potentially vaccine preventable infections. Vaccine 30:218-224. (PMID: 22100892)

Mendes, J. J., A. Marques-Costa, C. Vilela, J. Neves, N. Candeias, P. Cavaco-Silva, and J. Melo-Cristino. 2012. Clinical and bacteriological survey of diabetic foot infections in Lisbon. Diabetes Res Clin Pract 95:153-161. (PMID: 22019426)

Narciso, A., F. Nunes, T. Amores, L. Lito, J. Melo-Cristino, and A. Duarte. 2012. Persistence of uropathogenic Escherichia coli strains in the host for long periods of time: relationship between phylogenetic groups and virulence factors. Eur J Clin Microbiol Infect Dis. 31:1211–1217. (PMID: 21990017)

Costa, S. S., C. Falcao, M. Viveiros, D. Machado, M. Martins, J. Melo-Cristino, L. Amaral, and I. Couto. 2011. Exploring the contribution of efflux on the resistance to fluoroquinolones in clinical isolates of Staphylococcus aureus. BMC Microbiol 11:241. (PMID: 22032541)

Carreiro, A. V., O. Anunciação, J. A. Carriço, and S. C. Madeira. 2011. Prognostic prediction through biclustering-based classification of clinical gene expression time series. J Integr Bioinform 8:175 (PMID: 21926438)

Severiano A., F. R. Pinto, M. Ramirez, and J. A. Carriço. 2011. Adjusted Wallace as a measure of congruence between typing methods. J Clin Microbiol 49:3997-4000 (PMID: 21918028)

Martins E. R., A. Andreu, P. Correia, T. Juncosa, J. Bosch, M. Ramirez, and J. Melo-Cristino on behalf of the Microbiologist Group for the Study of Vertical Transmission Infections from the Catalan Society for Clinical Microbiology and Infectious Diseases. 2011. Group B streptococci causing neonatal infections in Barcelona are a stable clonal population: 18-year surveillance. J Clin Microbiol. 49:2911-2918 (PMID: 21697333)

Severiano A., J. A. Carriço, D. A. Robinson, M. Ramirez, and F. R. Pinto. 2011. Evaluation of jackknife and bootstrap for defining confidence intervals for pairwise agreement measures. PLoS ONE 6:e19539. (PMID: 21611165)

Hänscheid T., R. Romão, M. P. Grobusch, T. Amaral, and J. Melo-Cristino. 2011. Limitation of malaria diagnosis with the Cell-Dyn^® analyser: not all haemozoin-containing monocytes are detected or shown. Int J Lab Hematol 33:e14-16. (PMID: 21457189)

Frita R., M. Rebelo, A. Pamplona, A. M. Vigario, M. M. Mota, M. P. Grobusch, and T. Hänscheid. 2011. Simple flow cytometric detection of haemozoin containing leukocytes and erythrocytes for research on diagnosis, immunology and drug sensitivity testing. Malar. J 10:74. (PMID:21453521)

Nordmann P, Picazo JJ, Mutters R, Korten V, Quintana A, Laeuffer JM, Seak JC, Flamm RK, Morrissey I; on behalf of the COMPACT study group. 2011. Comparative activity of carbapenem testing: the COMPACT study. J Antimicrob Chemother. 66:1070-1078 (PMID: 21393160)

Hänscheid T., R. Badura, M. L. Fernandes, F. Antunes, and J. Melo-Cristino. 2011. The case of the disappearing mycobacteria in Ziehl-Neelsen-stained smears. Int. J. Infect. Dis 15:e291. (PMID: 21317005)

Sá-Leão R., F. Pinto, S. I. Aguiar, S. Nunes, J. A. Carriço, N. Frazão, N. Gonçalves-Sousa, J. Melo-Cristino, H. de Lencastre, and M. Ramirez. 2011. Analysis of invasiveness of pneumococcal serotypes and clones circulating in Portugal before widespread use of conjugate vaccines reveals heterogeneous behavior of clones expressing the same serotype. J. Clin. Microbiol 49:1369-1375. (PMID: 21270219)

Carrolo, M., Frias, M. J., F. R. Pinto, J. Melo-Cristino, and M. Ramirez. 2010. Prophage spontaneous activation promotes DNA release enhancing biofilm formation in Streptococcus pneumoniae. PLoS ONE 5:e15678. (PMID: 21187931)

Campuzano-Zuluaga G., T. Hanscheid, and M. P. Grobusch. 2010. Automated haematology analysis to diagnose malaria. Malar. J. 9:346. (PMID: 21118557)

Ramirez M., and J. Melo-Cristino. 2010. Expanding the diagnosis of pediatric bacteremic pneumococcal pneumonia from blood cultures to molecular methods: advantages and caveats. Clin. Infect. Dis 51:1050-1052.(PMID: 20883111)

Hänscheid T., and M. P. Grobusch. 2010. Biosafety and tuberculosis laboratories in Africa. Lancet Infect. Dis. 10:582-583. (PMID: 20797636)

McMillan D. J., D. E. Bessen, M. Pinho, C. Ford, G. S. Hall, J. Melo-Cristino, and M. Ramirez. 2010. Population genetics of Streptococcus dysgalactiae subspecies equisimilis reveals widely dispersed clones and extensive recombination. PLoS ONE 5:e11741. (PMID: 20668530)

Melo-Cristino J., L. Santos, C. Silva-Costa, A. Friães, M. D. Pinho, and M. Ramirez. 2010. The Viriato Study: Update on antimicrobial resistance of microbial pathogens responsible for community-acquired respiratory tract infections in Portugal. Paediatr. Drugs 12:11-17. (PMID: 20590169)

Aguiar S. I., M. J. Brito, J. Gonçalo-Marques, J. Melo-Cristino, and M. Ramirez. 2010. Serotypes 1, 7F and 19A became the leading causes of pediatric invasive pneumococcal infections in Portugal after 7 years of heptavalent conjugate vaccine use. Vaccine. 28:5167-73 (PMID: 20558247)

Pinho M. D., J. Melo-Cristino, and M. Ramirez. 2010. Fluoroquinolone resistance in Streptococcus dysgalactiae subsp. equisimilis and evidence for a shared global gene pool with Streptoccocus pyogenes. Antimicrob. Agents Chemother. 54:1769-1777. (PMID: 20145082)

Martins E. R., J. Melo-Cristino, and M. Ramirez. 2010. Evidence for rare capsular switching in Streptococcus agalactiae. J. Bacteriol. 192:1361-1369 (PMID: 20023016)

Brilha S., H. Proença, J. M. Cristino, and T. Hänscheid. 2010. Use of flow cytometry (Sysmex) UF-100) to screen for positive urine cultures: in search for the ideal cut-off. Clin. Chem. Lab. Med 48:289-292. (PMID: 19961394)

Simões A. S., R. Sá-Leão, M. J. Eleveld, D. A. Tavares, J. A. Carriço, H. J. Bootsma, and P. W. M. Hermans. 2010. Highly penicillin-resistant multidrug-resistant pneumococcus-like strains colonizing children in Oeiras, Portugal: genomic characteristics and implications for surveillance. J. Clin. Microbiol. 48:238-46 (PMID: 19906899)

Aguiar S. I., F. R. Pinto, S. Nunes, I. Serrano, J. Melo-Cristino, R. Sá-Leão, M. Ramirez, and H. de Lencastre. 2010. Increase of Denmark¹⁴-230 clone as a cause of pneumococcal infection in Portugal within a background of diverse serotype 19A lineages. J. Clin. Microbiol. 48:101–108. (PMID: 19864476)

Hänscheid T., R. Frita, M. Längin, P. G. Kremsner, and M. P. Grobusch. 2009. Is flow cytometry better in counting malaria pigment-containing leukocytes compared to microscopy? Malar. J 8:255. (PMID: 19917088)

Carrolo, M., F. R. Pinto, J. Melo-Cristino, and M. Ramirez. 2009. Pherotypes are driving genetic differentiation within Streptococcus pneumoniae. BMC Microbiol 9:191. (PMID: 19735561)

Earnshaw S., D. L. Monnet, B. Duncan, J. O'Toole, K. Ekdahl, H. Goossens, European Antibiotic Awareness Day Technical Advisory Committee, and European Antibiotic Awareness Day Collaborative Group. 2009. European Antibiotic Awareness Day, 2008 - the first Europe-wide public information campaign on prudent antibiotic use: methods and survey of activities in participating countries. Euro Surveill 14:19280. (PMID: 19643056)

Frias, M. J., J. Melo-Cristino, and M. Ramirez. 2009. The autolysin LytA contributes to efficient bacteriophage progeny release in Streptococcus pneumoniae. J. Bacteriol. 191:5428-5440. (PMID: 19581370)

Francisco, A. P., M. Bugalho, M. Ramirez, and J. A. Carriço. 2009. Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC Bioinformatics 10:152. (PMID: 19450271)

Hänscheid T, Längin M, Codices V, Luty AJ, Adegnika AA, Kremsner PG, Grobusch MP. Automated detection of haemozoin-containing monocytes for the diagnosis of malaria in microscopically negative cases during pregnancy. Acta Trop. 2009 Mar;109(3):245-6. (PMID: 19121281)

Pamplona A, Hanscheid T, Epiphanio S, Mota MM, Vigário AM. Cerebral malaria and the hemolysis/methemoglobin/heme hypothesis: shedding new light on an old disease. Int J Biochem Cell Biol. 2009 Apr;41(4):711-6. (PMID: 18930163)

Hänscheid T, Valadas E. Diagnosis of cryptosporidiosis using PCR or auramine O with LED fluorescent microscopy: which end of the stick? Acta Trop. 2009 Mar;109(3):247-8 (letter)

Trigo, G., P. Ferreira, N. Ribeiro, M. Dinis, E. B. Andrade, J. Melo-Cristino, M. Ramirez, and D. Tavares. 2008. Identification of immunoreactive extracellular proteins of Streptococcus agalactiae in bovine mastitis. Can. J. Microbiol. 54:899-905. (PMID: 18997846)

Pinto, F. R., J. Melo-Cristino, and M. Ramirez. 2008. A confidence interval for the Wallace coefficient of concordance and its application to microbial typing methods. PLoS ONE 3:e3696. (PMID: 19002246)

Aguiar, S. I., I. Serrano, F. R. Pinto, J. Melo-Cristino, M. Ramirez, and the Portuguese Surveillance Group for the Study of Respiratory Pathogens. 2008. Changes in Streptococcus pneumoniae serotypes causing invasive disease with non-universal vaccination coverage of the seven-valent conjugate vaccine. Clin. Microbiol. Infect. 14:835-843. (PMID: 18844684)

Silva-Costa, C., F. R. Pinto, M. Ramirez, J. Melo-Cristino, and the Portuguese Surveillance Group for the Study of Respiratory Pathogens. 2008. Decrease in macrolide resistance and clonal instability among Streptococcus pyogenes in Portugal. Clin. Microbiol. Infect. 14:1152-1159. (PMID: 19046174)

Pinto, F. R., S. I. Aguiar, J. Melo-Cristino, and M. Ramirez. 2008. Optimal control and analysis of two-color genomotyping experiments using bacterial multistrain arrays. BMC Genomics 9:230. (PMID: 18489741)

Aguiar, S. I., I. Serrano, F. R. Pinto, J. Melo-Cristino, and M. Ramirez. 2008. The presence of the pilus locus is a clonal property among pneumococcal invasive isolates. BMC Microbiol 8:41. (PMID: 18307767)

Faria, N. A., J. A. Carrico, D. C. Oliveira, M. Ramirez, and H. de Lencastre. 2008. Analysis of typing methods for epidemiological surveillance of both methicillin-resistant and methicillin-susceptible Staphylococcus aureus strains. J. Clin. Microbiol. 46:136-144. (PMID: 17989188)

Tavares, A., J. Inacio, J. Melo-Cristino, and I. Couto. 2008. Use of fluorescence in situ hybridization for rapid identification of staphylococci in blood culture samples collected in a Portuguese hospital. J Clin Microbiol 46:3097-3100.

Leitão, J. H., S. A. Sousa, M. V. Cunha, M. J. Salgado, J. Melo-Cristino, M. C. Barreto, and I. Sa-Correia. 2008. Variation of the antimicrobial susceptibility profiles of Burkholderia cepacia complex clonal isolates obtained from chronically infected cystic fibrosis patients: a five-year survey in the major Portuguese treatment center. Eur J Clin Microbiol Infect Dis 27:1101-1111

Hanscheid T, Melo Cristino J, Salgado MJ. Screening of auramine stained smears of all fecal samples is a rapid and inexpensive way to increase the detection of coccidial infections. 2008. Int J Infect Dis; 12(1):47-50.

Barbosa JM, Costa-de-Oliveira S, Rodrigues AG, Hanscheid T, Shapiro H, Pina-Vaz C. A flow cytometric protocol for detection of Cryptosporidium spp. 2008. Cytometry A; 73(1):44-7.

Hänscheid T. The future looks bright: low-cost fluorescent microscopes for detection of Mycobacterium tuberculosis and Coccidiae. 2008. Trans R Soc Trop Med Hyg; 102:520-1.

Shapiro HM, Hänscheid T. Fuchsin fluorescence in Mycobacterium tuberculosis: The Ziehl-Neelsen stain in a new light. 2008. J Microbiol Methods; 74: 119-120.

Vicente A, Barros R, Florinda A, Silva A, Hanscheid T. 2008. High rates of fluoroquinolone-resistant Campylobacter in Portugal–need for surveillance. Euro Surveill; 13. pii: 8031.

Hänscheid T, Längin M, Lell B, Pötschke M, Oyakhirome S, Kremsner PG, Grobusch MP. 2008. Full blood count and haemozoin-containing leukocytes in children with malaria: diagnostic value and association with disease severity. Malar J 12; 7:109.

Hänscheid T, Ribeiro CM, Shapiro HM, Perlmutter NG. Fluorescence microscopy for tuberculosis diagnosis. Lancet Infect Dis 7: 236-237.2007.

Hänscheid T, Egan TJ, Grobusch MP. Haemozoin: from melatonin pigment to drug target, diagnostic tool, and immune modulator. Lancet Infect Dis 7: 675-85. 2007.

M.V. Cunha, A. Pinto-de-Oliveira, L. Meirinho-Soares, M.J. Salgado, J. Melo-Cristino, S. Correia, C. Barreto, I. Sá-Correia. Excepcionally high representation of Burkholderia cepacia among B. cepacia complex isolates recovered from the major Portuguese Cystic Fibrosis Center. J Clin Microbiol 45: 1628-1633, 2007.

A. Friães, M. Ramirez, J. Melo-Cristino and the Portuguese group for the study of streptococcal infections. Non-outbreak surveillance of group A streptococci causing invasive disease in Portugal identified internationally disseminated clones among members of a genetically heterogeneous population. J Clin Microbiol 45: 2044-2047, 2007. (PMID: 17460058)

E.R. Martins, M.A. Pessanha, M. Ramirez, J. Melo-Cristino and the Portuguese Group for the Study of Streptococcal Infections. Analysis of Group B streptococcal isolates from infants and pregnant women in Portugal revealing two lineages with enhanced invasiveness. J Clin Microbiol 45: 3224-3229, 2007. (PMID: 17699641)

E.R. Martins, J. Melo-Cristino, M. Ramirez. Reevaluating the serotype II capsular locus of Streptococcus agalactiae. J Clin Microbiol 45: 3384-3386, 2007. (PMID: 17715372)

E.R. Martins, C. Florindo, F. Martins, I. Aldir, M.J. Borrego, L. Brum, M. Ramirez, J. Melo-Cristino. Streptococcus agalactiae serotype Ib as an agent of meningitis in two adult non-pregnant women. J Clin Microbiol 45: 3850-3852, 2007. (PMID: 17881554)

Pinto, F. R., J. A. Carriço, M. Ramirez, and J. S. Almeida. 2007. Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement. BMC Bioinformatics 8:44. (PMID: 17286861)

Pinho, M. D., J. Melo-Cristino, M. Ramirez, the Portuguese group for the study of streptococcal infections. 2006. Clonal relationships between invasive and noninvasive lancefield group C and G Streptococci and emm-specific differences in invasiveness. J. Clin. Microbiol. 44:841-846. (PMID: 16517864)

Silva-Costa, C., M. Ramirez, J. Melo-Cristino. 2006. Identification of macrolide-resistant clones of Streptococcus pyogenes in Portugal. Clin. Microbiol. Infect. 12:513-518. (PMID: 16700698)

Carriço, J.A., C. Silva-Costa, J. Melo-Cristino, F. R. Pinto, H. de Lencastre, J.S. Almeida, M. Ramirez. 2006. Illustration of a common framework for relating multiple typing methods by application to macrolide- resistant Streptococcus pyogenes. J. Clin. Microbiol. 44:2524-2532. (PMID: 16825375)

Serrano, I., J. Melo-Cristino, M. Ramirez. 2006. Heterogeneity of pneumococcal phase variants in invasive human infections. BMC Microbiol. 6:67. (PMID: 16872486)

Aguiar, S. I., M. J. Frias, L. Santos, J. Melo-Cristino, and M. Ramirez. 2006. Emergence of optochin resistance among Streptococcus pneumoniae in Portugal. Microb. Drug Resist. 12:239-245. (PMID: 17227208)

Figueiredo, T. A., S. I. Aguiar, J. Melo-Cristino, and M. Ramirez. 2006. DNA methylase activity as a marker for the presence of a family of phage-like elements conferring efflux-mediated macrolide resistance in streptococci. Antimicrob. Agents Chemother. 50:3689-3694. (PMID: 16954322)

Hanscheid T, Valadas E. Adequately performed stool ova and parasite examinations: is the best the enemy of the good? Clin Infect Dis. 2006;43:117-8.

Silva-Costa, C., M. Ramirez, and J. Melo-Cristino. 2005. Rapid inversion of the prevalences of macrolide resistance phenotypes paralleled by a diversification of T and emm types among Streptococcus pyogenes in Portugal. Antimicrob. Agents Chemother. 49:2109-2111. (PMID: 15855540)

Serrano, I., J. Melo-Cristino, J. A. Carriço, and M. Ramirez. 2005. Characterization of the genetic lineages responsible for pneumococcal invasive disease in Portugal. J. Clin. Microbiol. 43:1706-1715. (PMID: 15814989)

Hanscheid T, Monteiro C, Cristino JM, Lito LM, Salgado MJ. 2005. Growth of Mycobacterium tuberculosis in conventional BacT/ALERT FA blood culture bottles allows reliable diagnosis of Mycobacteremia. J. Clin. Microbiol. 43:890-891.

T. Conceição, A. Brizio, A. Duarte, L. M. Lito, J. Melo Cristino, M.J. Salgado. First description of CTX-M-15-producing Klebsiella pneumoniae in Portugal. Antimicrobial Agents and Chemotherapy 49: 477-478, 2005.

Conceição, T., N. Faria, L. Lito, J. Melo Cristino, M. J. Salgado, and A. Duarte. 2004. Diversity of chromosomal AmpC beta-lactamases from Enterobacter cloacae isolates in a Portuguese hospital. FEMS Microbiol Lett 230:197-202.

Conceição, T., N. Faria, M. Pimentel, G. Soveral, A. Duarte, L. M. Lito, J. Melo Cristino, and M. J. Salgado. 2004. New chromosomal AmpC beta-lactamase in Enterobacter cloacae. Antimicrob Agents Chemother 48:1437.

Figueira-Coelho, J., M. Ramirez, M. J. Salgado, and J. Melo-Cristino. 2004. Streptococcus agalactiae in a large Portuguese teaching hospital: antimicrobial susceptibility, serotype distribution, and clonal analysis of macrolide-resistant isolates. Microb Drug Resist 10:31-36. (PMID: 15140391)

Hänscheid, T., C. Monteiro, L. Marques-Lito, J. Melo-Cristino, and M. J. Salgado. 2004. Usefulness of Myco/F Lytic blood cultures (Bactec 9050) in the detection of Mycobacterium tuberculosis bacteraemia in HIV-infected patients in Portugal. Int J Infect Dis 8:253-254.

Serrano, I., M. Ramirez, The Portuguese Surveillance Group for the Study of Respiratory Pathogens, and J. Melo-Cristino. 2004. Invasive Streptococcus pneumoniae from Portugal: implications for vaccination and antimicrobial therapy. Clin Microbiol Infect 10:652-656. (PMID: 15214879)

Valadas, E., T. Hänscheid, and F. Antunes. 2004. HIV Infection and non-tuberculous mycobacteria: how important in southern European countries? Scand J Infect Dis 36:685-686.

Zé-Zé, L., R. Tenreiro, A. Duarte, M. J. Salgado, J. Melo-Cristino, L. Lito, M. M. Carmo, S. Felisberto, and G. Carmo. 2004. Case of aortic endocarditis caused by Lactobacillus casei. J Med Microbiol 53:451-453.

J. Melo Cristino, M. Ramirez, N. Serrano, T. Hänscheid, and The Portuguese Surveillance Group for the Study of Respiratory Pathogens. 2003. Macrolide resistance in Streptococcus pneumoniae isolated from patients with community-acquired lower respiratory tract infections in Portugal: Results of a 3-year (1999-2001) multicenter surveillance study Microbial Drug Resistance 9: 73-80. (PMID: 12705685)

T. Hänscheid, B.G. Pinto, J. Melo Cristino, M.P. Grobusch. 2003. Avoiding misdiagnosis of imported malaria: screening of emergency room samples with thrombocytopenia detects clinically unsuspected cases. Journal of Travel Medicine 10: 155-157.

A. Duarte, F. Boavida, F. Grosso, M. Correia, L.M. Lito, J. Melo Cristino, M.J. Salgado. Outbreak of GES-1 beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae in a University Hospital in Lisbon, Portugal. Antimicrob Agents Chemother 47:1481-1482.

M. Correia, F. Boavida, F. Grosso, M.J. Salgado, L.M. Lito, J. Melo Cristino, S. Mendo, A. Duarte. 2003. Molecular characterization of a new class 3 integron in Klebsiella pneumoniae”. Antimicrob Agents Chemother 47:2838-2843, 2003.

Grobusch PM, Hänscheid T, Göbels K, Slevogt H, Zoller T, Rögler G, Teichmann D. Comparison of three antigen detection tests for diagnosis and follow-up of falciparum malaria in travellers returning to Berlin, Germany. Parasitol Res 2003; 89: 354-357

Hänscheid T. 2003. Update: Current strategies to avoid misdiagnosis of malaria. Clin Microbiol Infect 203; 997-504

Grobusch MP, Hänscheid T, Krämer B, Neukammer J, May J, Seybold J, Kun JFJ, Suttorp N. 2003. Diagnosis of malaria by automated detection of malaria pigment in travelers returning to Berlin, Germany. Cytometry 55B(1):46-51.

Valadas E, T, Fernandes ML, Antunes F. 2003. Smear microsocopy to diagnose tuberculosis early and prevent further transmission in a population with a high prevelance of HIV infection. Clin Microbiol Infect 2003; 9(10):1045-1047

Brito, D. A., M. Ramirez and H. de Lencastre. 2003. Serotyping Streptococcus pneumoniae by multiplex PCR. J. Clin. Microbiol. 41:2378-2384. (PMID: 12791852)