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Papers

 

 

PAPERS

  1. Balbontín R, Frazão N, Gordo I. 2019. DNA breaks-mediated cost reveals RNase HI as a new target for selectively eliminating antibiotic resistance. BioRxiv 756767. doi: 10.1101/756767
  2. Ballesteros-Arias L, Silva JG, Paiva RA, Carbonetto B, Faísca P, Martins VC. 2019. T cell acute lymphoblastic leukemia as a consequence of thymus autonomy. J Immunol. Feb 15;202(4):1137-1144. doi: 10.4049/jimmunol.1801373
  3. Barreto HC, Sousa A, Gordo I. 2019. The landscape of adaptive evolution of a gut commensal bacteria in aging mice. Current Biology. doi: 10.1016/j.cub.2020.01.037
  4. Barroso-Batista J, Pedro MF, Sales-Dias J, Pinto CJG, Pereira H, Demengeot J, Gordo I, Xavier K. 2019. Specific eco-evolutionary contexts in the mouse gut reveal Escherichia coli metabolic versatility. Current Biology (2020), doi: 10.1016/j.cub.2020.01.050
  5. Cardoso LL, Durão P, Amicone M, Gordo I. 2019. Dysbiosis personalizes fitness effect of antibiotic resistance in the mammalian gut. Biorxiv 748897. doi: 10.1101/748897
  6. Carriço JA, Crochemore M, Francisco AP, Pissis SP, Ribeiro-Gonçalves B, Vaz C. 2018. Fast phylogenetic inference from typing data. Algorithms Mol Biol. Feb 15;13:4. doi: 10.1186/s13015-017-0119-7
  7. Carriço JA, Rossi M, Moran-Gilad J, Van Domselaar G, Ramirez M. 2018. A primer on microbial bioinformatics for nonbioinformaticians. Clin Microbiol Infect. Apr;24(4):342-349. doi: 10.1016/j.cmi.2017.12.015
  8. Chung M, Borges V, Gomes JP, de Lencastre H, Tomasz A. 2018. Phenotypic signatures and genetic determinants of oxacillin tolerance in a laboratory mutant of Staphylococcus aureus. PLoS One. Jul 3;13(7):e0199707. doi: 10.1371/journal.pone.0199707
  9. Coelho I, Duarte N, Macedo MP, Penha-Gonçalves C. 2019. Trem-2 modulation of gut microbiota is blunted during hepatotoxic injury and uncoupled from liver repair responses. BioRxiv 857078. doi: 10.1101/857078
  10. Coelho I, Duarte N, Barros A, Macedo MP, Penha-Gonçalves C. 2019. Trem-2 promotes emergence of restorative macrophages and endothelial cells during recovery from hepatic tissue damage. BioRxiv 823773. doi: 10.1101/823773
  11. Conceição T, Martins H, Rodrigues S, de Lencastre H, Aires-de-Sousa M. 2019. Staphylococcus aureus nasal carriage among homeless population in Lisbon, Portugal. Eur J Clin Microbiol Infect Dis. Jul 22. doi: 10.1007/s10096-019-03638-4
  12. Culebro A, Machado MP, Carriço JA, Rossi M. 2018. Origin, evolution, and distribution of the molecular machinery for biosynthesis of sialylated lipooligosaccharide structures in Campylobacter coli. Sci Rep. Feb 14;8(1):3028. doi: 10.1038/s41598-018-21438-2
  13. Durão P, Balbontín R, Gordo I. 2018. Evolutionary mechanisms shaping the maintenance of antibiotic resistance. Trends Microbiol. 26 (8):677-691. doi: 10.1016/j.tim.2018.01.005
  14. 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 MR, Ramirez M. 2019. Streptococcus pneumoniae serotype 3 in Mexico (1994-2017): decrease of the unusual CC4909 lineage post-PCV13 introduction. J Clin Microbiol. Jan 2;57(1) doi: 10.1128/JCM.01354-18
  15. Espadinha D, Sobral RG, Mendes CI, Méric G, Sheppard SK, Carriço JA, de Lencastre H, Miragaia M. 2019. Distinct phenotypic and genomic signatures underlie contrasting pathogenic potential of Staphylococcus epidermidis clonal lineages. Front. Microbiol. Aug 27; 10:1971. doi: 10.3389/fmicb.2019.01971
  16. Esteves AM, Graça G, Peyriga L, Torcato IM, Borges N, Portais JC, Santos H. 2019. Combined transcriptomics-metabolomics profiling of the heat shock response in the hyperthermophilic archaeon Pyrococcus furiosus. Extremophiles. Jan;23(1):101-118. doi: 10.1007/s00792-018-1065-0
  17. Garriss G, Nannapaneni P, Simões AS, Browall S, Subramanian K, Sá-Leão R, Goossens H, de Lencastre H, Henriques-Normark B. 2019. Genomic characterization of the emerging pathogen Streptococcus pseudopneumoniae. mBio Jun 25;10(3). doi: 10.1128/mBio.01286-19
  18. Graça-Lopes G, Graça G, Barahona S, Moreira RN, Arraiano CM, Gonçalves LG. 2019. NMR-metabolomics shows that BolA is an important modulator of Salmonella typhimurium metabolic processes under virulence conditions. Metabolites. 9 (11), 243. doi:10.3390/metabo9110243
  19. Godinho-Santos A, Foxall R B, Antão AV, Tavares B, Ferreira T, Serra-Caetano A, Matoso P, Sousa AE. 2020. Follicular helper T cells are major HIV-2 reservoirs and support productive infection. J Infect Dis. 221:1. doi:10.1093/infdis/jiz431
  20. Gomes LP, Anjo SI, Manadas B, Coelho AV, Paschoalin VMF. 2020. Proteomic analyses reveal new insights on the antimicrobial mechanisms of chitosan biopolymers and their nanosized particles against Escherichia coli. Int. J. Mol. Sci. 2020, 21, 225; doi:10.3390/ijms21010225
  21. Gonçalves BV, Portela R, Lobo R, Figueiredo TA, Grilo IR, Ludovice AM, de Lencastre H, Dias JS, Sobral RG. 2019. The role of MurT C-terminal domain in the amidation of Staphylococcus aureus peptidoglycan. Antimicrob Agents Chemother, 63 (10) e00957-19. doi:10.1128/AAC.00957-19
  22. Hiller NL, Sá-Leão R. 2018. Puzzling over the pneumococcal pangenome. Front. Microbiol. 9:2580. doi: 10.3389/fmicb.2018.02580
  23. Isidro J, Menezes J, Serrano M, Borges V, Paixão P, Mimoso M, Martins F, Toscano C, Santos A, Henriques AO and Oleastro M. 2018. Genomic study of a Clostridium difficile multidrug resistant outbreak-related clone reveals novel determinants of resistance. Front Microbiol 9:2994. doi: 10.3389/fmicb.2018.02994
  24. 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 Research, 47 (D1),–D194, doi: 10.1093/nar/gky1073.
  25. Lopes E, Fernandes T, Machado MP, Carriço JA, Melo-Cristino J, Ramirez M, Martins ER, the Portuguese Group for the Study of Streptococcal Infections. 2018. 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 
  26. Miragaia M. 2018. Factors contributing to the evolution of mecA-mediated-lactam resistance in Staphylococci: Update and new insights rrom whole genome sequencing (WGS). Front. Microbiol. 9:2723. doi: 10.3389/fmicb.2018.02723
  27. 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. Microbial Genomics. doi: 10.1099/mgen.0.000328
  28. Nunes F, Fernandes C, Freitas C, Marini E, Serrano M, Moran Jr CP, Eichenberger P, Henriques AO. 2018. SpoVID functions as a non-competitive hub that connects the modules for assembly of the inner and outer spore coat layers in Bacillus subtilis. Mol Microbiol, 110: 576-595. doi: 10.1111/mmi.14116
  29. Oliveira RA, Ng KM, Correia MB, Cabral V, Shi H, Sonnenburg JL, Huang KC, Xavier KB. 2020 vby nutrition competition. Nat Microbiol (2020). https://doi.org/10.1038/s41564-019-0658-4
  30. Pardos de la Gandara M, Borges V, Chung M, Milheiriço C, Gomes JP, de Lencastre H, Tomasz A. 2018. Genetic determinants of high-level oxacillin resistance in methicillin resistant Staphylococcus aureus. Antimicrob Agents Chemother 62 (6) e00206-18. doi: 10.1128/AAC.00206-18
  31. Pereira FC, Nunes F, Cruz F, Fernandes C, Isidro AL, Lousa D, Soares CM, Moran CP, Jr, Henriques AO, Serrano M. 2019. A LysM domain intervenes in sequential proteinprotein and protein-peptidoglycan interactions important for spore coat assembly in Bacillus subtilis. J Bacteriol 201 (4) e00642-18. doi: 10.1128/JB.00642-18
  32. Pinho MD, Foster G, Pomba C, Machado MP, Baily JL, Kuiken T, Melo-Cristino J, Ramirez M and the 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
  33. Pobre V, Arraiano CM. 2018. Characterizing the role of exoribonucleases in the control of microbial gene expression: Differential RNA-Seq. Methods Enzymol. 2018;612:1-24. doi: 10.1016/bs.mie.2018.08.010
  34. Pobre V, Barahona S, Dobrzanski T, Steffens MBR, Arraiano, CM. 2019. Defining the impact of exoribonucleases in the shift between exponential and stationary phases. Sci Rep 9, 16271. doi:10.1038/s41598-019-52453-6
  35. Reichmann NT, Tavares AC, Saraiva BM, Jousselin A, Reed P, Pereira AR, Monteiro JM, Sobral RG, VanNieuwenhze MS, Fernandes F, Pinho, MG. 2019. SEDS–bPBP pairs direct lateral and septal peptidoglycan synthesis in Staphylococcus aureus. Nature microbiology, 1. doi: 10.1038/s41564-019-0437-2
  36. Ribeiro TG, Ribeiro-Gonçalves B, da Silva MS, Novais A, Machado E, Carriço JA, Peixe L. 2017. Citrobacter portucalensis sp. nov., isolated from an aquatic sample . Int J Syst Evol Microbiol. 67(9):3513-3517. doi: 10.1099/ijsem.0.002154
  37. 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
  38. Tavares DA, Handem S, Carvalho RJ, Paulo AC, de Lencastre H, Hinds J, Sá-Leão R. 2019. Identification of Streptococcus pneumoniae by a real-time PCR assay targeting SP2020. Scientific reports, 9(1), 3285. doi: 10.1038/s41598-019-39791-1
  39. Vaz F, Kounatidis I, Covas G, Parton RM, Harkiolaki M, Davis I, Filipe SR, Ligoxygakis P. 2019. Accessibility to peptidoglycan is important for the recognition of Gram-Positive bacteria in Drosophila. Cell reports, 27(8), 2480-2492. doi: 10.1016/j.celrep.2019.04.103
  40. Vieira FJD, Nadal-Jimenez P, Teixeira L, Xavier KB. 2019. Quorum sensing regulation in Erwinia carotovora affects development of Drosophila melanogaster infected larvae. BioRxiv 2019.12.13.876318. doi: 10.1101/2019.12.13.876318
  41. Yu K, Matzapetakis M, Valent D, Saco Y, de Almeida AM, Terré M, Bassols A. 2018. Skeletal muscle metabolomics and blood biochemistry analysis reveal metabolic changes associated with dietary amino acid supplementation in dairy calves. Sci Rep. 14;8(1):13850. doi: 10.1038/s41598-018-32241-4

 

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