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--- publications [2019/01/09 10:04]
ramirez [2019]
+++ publications [2019/05/23 10:12]
ramirez [2018]
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 ===== 2019  =====
-Echániz-Aviles G, Guerreiro SI, [[people:anacosta|Silva-Costa C]], [[people:cmendes|Mendes CI]], [[people:jcarrico|Carriço JA]], Carnalla-Barajas MN, Soto-Noguerón A, Velazquez-Meza ME, [[people:jmelocristino|Melo-Cristino J]], Luévanos-Velazquez A, Martínez-Medina L, Vázquez-Larios MDR, [[people:ramirez|Ramirez M]]. 2018. <fc #0000FF>//Streptococcus pneumoniae// serotype 3 in Mexico (1994-2017): decrease of the unusual CC4909 lineage post-PCV13 introduction</fc>. J Clin Microbiol. 57 e01354-18 [[https://doi.org/10.1128/JCM.01354-18|doi:10.1128/JCM.01354-18]] [[http://www.ncbi.nlm.nih.gov/pubmed/30404945|(PMID: 30404945)]]
+Caneiras C, Lito L, [[people:jmelocristino|Melo-Cristino J]], Duarte A. 2019. <fc #0000FF>Community- and hospital-acquired Klebsiella pneumoniae urinary tract infections in Portugal: virulence and antibiotic resistance</fc>. Microorganisms 7:138. [[https://doi.org/10.3390/microorganisms7050138|doi:10.3390/microorganisms7050138]]
-Pinto M, González-Díaz A, [[people:mpmachado|Machado MP]], Duarte S, Vieira L, [[people:jcarrico|Carriço JA]], Marti S, Bajanca-Lavado MP, Gomes JP. 2018. <fc #0000FF>Insights into the population structure and pan-genome of //Haemophilus influenzae//</fc>. Infect Genet Evol. 67:126–135 [[http://www.ncbi.nlm.nih.gov/pubmed/30391557|(PMID: 30391557)]]
+[[people:mdpinho|Pinho MD]], Foster G, Pomba C, [[people:mpmachado|Machado MP]], Baily JL, Kuiken T, [[people:jmelocristino|Melo-Cristino J]], [[people:ramirez|Ramirez M]], Portuguese Group for the Study of Streptococcal Infections. 2019. <fc #0000FF>//Streptococcus canis// are a single population infecting multiple animal hosts despite the diversity of the universally present M-like protein SCM</fc>. Front Microbiol 10:631.[[https://doi.org/10.3389/fmicb.2019.00631|doi:10.3389/fmicb.2019.00631]] [[http://www.ncbi.nlm.nih.gov/pubmed/30984150|(PMID: 30984150)]]
+[[people:anacosta|Silva-Costa C]], Brito MJ, Aguiar SI, Lopes JP, [[people:ramirez|Ramirez M]], [[people:jmelocristino|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. <fc #0000FF>Dominance of vaccine serotypes in pediatric invasive pneumococcal infections in Portugal (2012-2015)</fc>. Sci Rep 9:6. [[https://doi.org/10.1038/s41598-018-36799-x|doi:10.1038/s41598-018-36799-x]] [[http://www.ncbi.nlm.nih.gov/pubmed/30626918|(PMID: 30626918)]]
+Echániz-Aviles G, Guerreiro SI, [[people:anacosta|Silva-Costa C]], [[people:cmendes|Mendes CI]], [[people:jcarrico|Carriço JA]], Carnalla-Barajas MN, Soto-Noguerón A, Velazquez-Meza ME, [[people:jmelocristino|Melo-Cristino J]], Luévanos-Velazquez A, Martínez-Medina L, Vázquez-Larios MDR, [[people:ramirez|Ramirez M]]. 2019. <fc #0000FF>//Streptococcus pneumoniae// serotype 3 in Mexico (1994-2017): decrease of the unusual CC4909 lineage post-PCV13 introduction</fc>. J Clin Microbiol. 57 e01354-18 [[https://doi.org/10.1128/JCM.01354-18|doi:10.1128/JCM.01354-18]] [[http://www.ncbi.nlm.nih.gov/pubmed/30404945|(PMID: 30404945)]]
+Pinto M, González-Díaz A, [[people:mpmachado|Machado MP]], Duarte S, Vieira L, [[people:jcarrico|Carriço JA]], Marti S, Bajanca-Lavado MP, Gomes JP. 2019. <fc #0000FF>Insights into the population structure and pan-genome of //Haemophilus influenzae//</fc>. Infect Genet Evol. 67:126–135 [[http://www.ncbi.nlm.nih.gov/pubmed/30391557|(PMID: 30391557)]]
+Jesus TF, [[people:bgoncalves|Ribeiro-Gonçalves B]], Silva DN, Bortolaia V, [[people:ramirez|Ramirez M]], [[people:jcarrico|Carriço JA]]. 2019. <fc #0000FF>Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data</fc>. Nucleic Acids Res 47:D188–D194 [[http://www.ncbi.nlm.nih.gov/pubmed/30395323|(PMID: 30395323)]]
 ===== 2018  =====
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 Caneiras C, Calisto F, Jorge da Silva G, Lito L, [[people:jmelocristino|Melo-Cristino J]], Duarte A. 2018. <fc #0000FF>First description of colistin and tigecycline-resistant //Acinetobacter baumannii// producing KPC-3 carbapenemase in Portugal</fc>. Antibiotics 7. [[https://doi.org/10.3390/antibiotics7040096|doi:10.3390/antibiotics7040096]] [[http://www.ncbi.nlm.nih.gov/pubmed/30404152|(PMID: 30404152)]]
-Jesus TF, [[people:bgoncalves|Ribeiro-Gonçalves B]], Silva DN, Bortolaia V, [[people:ramirez|Ramirez M]], [[people:jcarrico|Carriço JA]]. 2018. <fc #0000FF>Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data</fc>. Nucleic Acids Res. //In press// [[https://doi.org/10.1093/nar/gky1073|doi:10.1093/nar/gky1073]] [[http://www.ncbi.nlm.nih.gov/pubmed/30395323|(PMID: 30395323)]]
 [[people:ahoracio|Horácio AN]], [[people:anacosta|Silva-Costa C]], Lopes E, [[people:ramirez|Ramirez M]], [[people:jmelocristino|Melo-Cristino J]], Portuguese Group for the Study of Streptococcal Infections. 2018. <fc #0000FF>Conjugate vaccine serotypes persist as major causes of non-invasive pneumococcal pneumonia in Portugal despite declines in serotypes 3 and 19A (2012-2015)</fc>. PLoS ONE 13:e0206912.[[https://doi.org/10.1371/journal.pone.0206912|doi:10.1371/journal.pone.0206912]] [[http://www.ncbi.nlm.nih.gov/pubmed/30388168|(PMID: 30388168)]]
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 [[people:cpato|Pato C]], [[people:jmelocristino|Melo-Cristino J]], [[people:ramirez|Ramirez M]], [[people:afriaes|Friães A]], Portuguese Group for the Study of Streptococcal Infections. 2018. <fc #0000FF>//Streptococcus pyogenes// causing skin and soft tissue infections are enriched in the recently emerged //emm//89 clade 3 and are not associated with abrogation of CovRS</fc>. Front Microbiol 9:2372.[[http://www.ncbi.nlm.nih.gov/pubmed/30356787|(PMID: 30356787)]]
-Björnsdóttir ES, [[people:emartins|Martins ER]], Erlendsdóttir H, Haraldsson G, [[people:jmelocristino|Melo-Cristino J]], [[people:ramirez|Ramirez M]], Kristinsson KG. 2018. <fc #0000FF>Group B streptococcal neonatal and early infancy infections in Iceland 1976 - 2015</fc>. Pediatr Infect Dis J. //In press// [[http://www.ncbi.nlm.nih.gov/pubmed/30299423|(PMID: 30299423)]] [[https://doi.org/10.1097/INF.0000000000002214|doi:10.1097/INF.0000000000002214]]
 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. 2018. <fc #0000FF>A modified case definition to facilitate essential hospital care during Ebola outbreaks</fc>. Clin Infect Dis. //In press// [[http://www.ncbi.nlm.nih.gov/pubmed/30239602|(PMID: 30239602)]] [[https://doi.org/10.1093/cid/ciy798|doi:10.1093/cid/ciy798]]
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 Barreto JN, de Lourdes Monteiro M, da Luz Lima M, Valadas E, Hänscheid T. 2018. <fc #0000FF>Under-reporting of tuberculosis in Praia, Cape Verde: study reports doubtful results</fc>. Int J Tuberc Lung Dis 22:1106. [[http://www.ncbi.nlm.nih.gov/pubmed/30092879|(PMID: 30092879)]]
-Branco A, Francisco D, Hänscheid T. 2018. <fc #0000FF>Is there a “normal” oxygen concentration for in vitro //Plasmodium// cultures?</fc> Trends Parasitol. //In press// [[http://www.ncbi.nlm.nih.gov/pubmed/30049603|(PMID: 30049603)]]
+Branco A, Francisco D, Hänscheid T. 2018. <fc #0000FF>Is there a “normal” oxygen concentration for in vitro //Plasmodium// cultures?</fc> Trends Parasitol 34:811–812. [[http://www.ncbi.nlm.nih.gov/pubmed/30049603|(PMID: 30049603)]]
 Hänscheid T, Grobusch MP. 2018. <fc #0000FF>Could antibiotic treatment of traveller’s diarrhoea even prolong elimination of pathogens?</fc> Travel Med Infect Dis. //In press// [[http://www.ncbi.nlm.nih.gov/pubmed/30030070|(PMID: 30030070)]]
@@ Line 35: / Line 40: @@
 Zhou Z, Alikhan NF, Sergeant MJ, Luhmann N, Vaz C, Francisco AP, [[people:jcarrico|Carriço JA]], Achtman M.<fc #0000FF> GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. </fc> Genome Res. 2018 Sep;28(9):1395-1404. doi: 10.1101/gr.232397.117. Epub 2018 Jul 26. [[http://www.ncbi.nlm.nih.gov/pubmed/30049790|(PMID: 30049790)]]
-Teixeira AS, Monteiro PT, [[people:jcarrico|Carriço JA]], Santos FC, Francisco AP. <fc #0000FF>Large-scale simulations of bacterial populations over complex networks</fc>. J Comput Biol. 2018; //In press//. doi:10.1089/cmb.2018.0083 [[http://www.ncbi.nlm.nih.gov/pubmed/29985650|(PMID: 29985650)]]
+Teixeira AS, Monteiro PT, [[people:jcarrico|Carriço JA]], Santos FC, Francisco AP. 2018. <fc #0000FF>Large-scale simulations of bacterial populations over complex networks</fc>. J Comput Biol 25:850–861. [[http://www.ncbi.nlm.nih.gov/pubmed/29985650|(PMID: 29985650)]]
-[[people:anacosta|Silva-Costa C]], Brito MJ, [[people:mdpinho|Pinho MD]], [[people:afriaes|Friães A]], Aguiar SI, [[people:ramirez|Ramirez M]], [[people:jmelocristino|Melo-Cristino J]], Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Invasive Pneumococcal Disease of the Pediatric Infectious Disease Society. <fc #0000FF>Pediatric complicated pneumonia caused by //Streptococcus pneumoniae// serotype 3 in 13-valent pneumococcal conjugate vaccinees, Portugal, 2010-2015</fc>. Emerging Infect Dis. 2018;24: 1307–1314. doi:10.3201/eid2407.180029 [[http://www.ncbi.nlm.nih.gov/pubmed/29912700|(PMID: 29912700)]]
+[[people:anacosta|Silva-Costa C]], Brito MJ, [[people:mdpinho|Pinho MD]], [[people:afriaes|Friães A]], Aguiar SI, [[people:ramirez|Ramirez M]], [[people:jmelocristino|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. <fc #0000FF>Pediatric complicated pneumonia caused by //Streptococcus pneumoniae// serotype 3 in 13-valent pneumococcal conjugate vaccinees, Portugal, 2010-2015</fc>. Emerging Infect Dis 24: 1307–1314. [[http://www.ncbi.nlm.nih.gov/pubmed/29912700|(PMID: 29912700)]]
 Grobusch MP, Schaumburg F, Weitzel T, Rothe C, Hänscheid T, Goorhuis A. 2018. <fc #0000FF>Ebola 2018 - Implications for travel health advice and relevance for travel medicine</fc>. Travel Med Infect Dis 24:1–3. [[http://www.ncbi.nlm.nih.gov/pubmed/29906571|(PMID: 29906571)]]
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 Hänscheid T, Hardisty DW. 2018. <fc #0000FF>How “resistant” is artemisinin resistant malaria? - The risks of ambiguity using the term “resistant” malaria</fc>. Travel Med Infect Dis 24:23–24. [[http://www.ncbi.nlm.nih.gov/pubmed/29715560|(PMID: 29715560)]]
-Motro Y, [[people:jcarrico|Carriço JA]], Friedrich AW, Rossen JW, Moran-Gilad J.<fc #0000FF> ESCMID Postgraduate Education Course Regional Capacity Building for Integration of Next-Generation Sequencing in the Clinical Microlab.</fc> Microbes Infect. 2018 Mar 16. pii: S1286-4579(18)30050-9. doi: 10.1016/j.micinf.2018.02.006. [Epub ahead of print]  [[http://www.ncbi.nlm.nih.gov/pubmed/29555344 |(PMID: 29555344)]]
+Motro Y, [[people:jcarrico|Carriço JA]], Friedrich AW, Rossen JW, Moran-Gilad J. 2018.<fc #0000FF> ESCMID Postgraduate Education Course Regional Capacity Building for Integration of Next-Generation Sequencing in the Clinical Microlab.</fc> Microbes Infect 20:275–280. [[http://www.ncbi.nlm.nih.gov/pubmed/29555344 |(PMID: 29555344)]]
 Silva M, [[people:mpmachado|Machado MP]], Silva DN, Rossi M, Moran-Gilad J, Santos S, [[people:ramirez|Ramirez M]], [[people:jcarrico|Carriço JA]]. <fc #0000FF> chewBBACA: A complete suite for gene-by-gene schema creation and strain identification.</fc> Microb Genom. 2018 Mar 15. doi: 10.1099/mgen.0.000166. [Epub ahead of print] [[http://www.ncbi.nlm.nih.gov/pubmed/29543149 |(PMID: 29543149)]]