M. Ramirez

发表

Not Seeing the Forest for the Trees: Size of the Minimum Spanning Trees (MSTs) Forest and Branch Significance in MST-Based Phylogenetic Analysis

Alexandre P. Francisco, Pedro T. Monteiro, Andreia Sofia Teixeira, 2015, PloS one.

iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6

I. Rocha, M. Ramirez, Oscar Días, 2019, Front. Microbiol..

Artigo Original Original Article

M. Ramirez, L. Santos, Letícia Santos, 2013 .

The presence of the pilus locus is a clonal property among pneumococcal invasive isolates

M. Ramirez, J. Melo-Cristino, S. Aguiar, 2008, BMC Microbiology.

Evidence for the geographic spread of a methicillin-resistant Staphylococcus aureus clone between Portugal and Spain

A. Tomasz, M. Ramirez, H. de Lencastre, 1995, Journal of clinical microbiology.

Analysis of Typing Results

João André Carriço, M. Ramirez, 2014 .

Adjusted Wallace Coefficient as a Measure of Congruence between Typing Methods

João André Carriço, M. Ramirez, Francisco R. Pinto, 2011, Journal of Clinical Microbiology.

Analysis of Group B Streptococcal Isolates from Infants and Pregnant Women in Portugal Revealing Two Lineages with Enhanced Invasiveness

M. Ramirez, J. Melo-Cristino, E. Martins, 2007, Journal of Clinical Microbiology.

Nonoutbreak Surveillance of Group A Streptococci Causing Invasive Disease in Portugal Identified Internationally Disseminated Clones among Members of a Genetically Heterogeneous Population

M. Ramirez, J. Melo-Cristino, A. Friães, 2007, Journal of Clinical Microbiology.

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.

M. Ramirez, M. Brito, J. Melo-Cristino, 2014, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

Pherotype Influences Biofilm Growth and Recombination in Streptococcus pneumoniae

M. Ramirez, J. Melo-Cristino, Francisco R. Pinto, 2014, PloS one.

Faecal shedding and serological cross-sectional study of Lawsonia intracellularis in horses in the state of Minas Gerais, Brazil.

M. Ramirez, R. Guedes, C. V. Guimarães-Ladeira, 2009, Equine veterinary journal.

Acquisition of new capsular genes among clinical isolates of antibiotic-resistant Streptococcus pneumoniae.

A. Tomasz, M. Ramirez, A. Tomasz, 1999, Microbial drug resistance.

Evidence for Rare Capsular Switching in Streptococcus agalactiae

M. Ramirez, J. Melo-Cristino, E. Martins, 2009, Journal of bacteriology.

Streptococcus pneumoniae Isolates with Reduced Susceptibility to Ciprofloxacin in Spain: Clonal Diversity and Appearance of Ciprofloxacin-Resistant Epidemic Clones

M. Ramirez, H. de Lencastre, C. García-rey, 2001, Antimicrobial Agents and Chemotherapy.

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

M. Ramirez, J. Melo-Cristino, A. Horácio, 2016, Front. Microbiol..

Characteristics of Streptococcus agalactiae Colonizing Nonpregnant Adults Support the Opportunistic Nature of Invasive Infections

M. Ramirez, J. Melo-Cristino, E. Martins, 2022, Microbiology spectrum.

Heterogeneity of penicillin-non-susceptible group B streptococci isolated from a single patient in Germany

João André Carriço, M. P. van der Linden, M. Ramirez, 2019, The Journal of antimicrobial chemotherapy.

Changes in emm types and superantigen gene content of Streptococcus pyogenes causing invasive infections in Portugal

M. Ramos, P. Paixão, M. Ramirez, 2019, Scientific Reports.

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

João André Carriço, M. Ramirez, M. Machado, 2018, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

A widespread family of polymorphic toxins encoded by temperate phages

M. Touchon, E. Rocha, João André Carriço, 2017, BMC Biology.

Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens

Tiago F Jesus, A. Friedrich, João André Carriço, 2018, Scientific Reports.

Capsule impairs efficient adherence of Streptococcus agalactiae to intestinal epithelium in tilapias Oreochromis sp.

M. Ramirez, J. Melo-Cristino, C. Iregui, 2016, Microbial pathogenesis.

Conjugate vaccine serotypes persist as major causes of non-invasive pneumococcal pneumonia in Portugal despite declines in serotypes 3 and 19A (2012-2015)

M. Ramirez, J. Melo-Cristino, A. Horácio, 2018, PloS one.

Ubiquitous distribution of the competence related genes comA and comC among isolates of Streptococcus pneumoniae.

A. Tomasz, D. Morrison, M. Ramirez, 1997, Microbial drug resistance.

Macrolide-resistant Streptococcus pyogenes: prevalence and treatment strategies

M. Ramirez, J. Melo-Cristino, A. Friães, 2015, Expert review of anti-infective therapy.

Macrolide-resistant Streptococcus pyogenes: prevalence and treatment

M. Ramirez, J. Melo-Cristino, C. Silva-Costa, 2015 .

Scarlet Fever Is Caused By a Limited Number of Streptococcus pyogenes Lineages and Is Associated with the Exotoxin Genes ssa, speA and speC

João André Carriço, M. Ramirez, J. Melo-Cristino, 2014, The Pediatric infectious disease journal.

Pathogenesis and host ResPonse

João André Carriço, M. Ramirez, J. Melo-Cristino, 2022 .

Molecular analysis of the promoter region of the hexokinase 2 gene of Saccharomyces cerevisiae.

C. Martínez-Campa, P. Herrero, F. Moreno, 1996, FEMS microbiology letters.

Distribution of Pilus Islands in Streptococcus agalactiae That Cause Human Infections: Insights into Evolution and Implication for Vaccine Development

M. Ramirez, A. Andreu, J. Melo-Cristino, 2012, Clinical and Vaccine Immunology.

Pediatric Complicated Pneumonia Caused by Streptococcus pneumoniae Serotype 3 in 13-Valent Pneumococcal Conjugate Vaccinees, Portugal, 2010–2015

M. Ramirez, M. Brito, J. Melo-Cristino, 2018, Emerging infectious diseases.

Export of the pneumococcal phage SV1 lysin requires choline‐containing teichoic acids and is holin‐independent

M. Ramirez, J. Melo-Cristino, M. J. Frias, 2013, Molecular microbiology.

Molecular Epidemiology of Streptococcus pneumoniae

João André Carriço, M. Ramirez, J. Melo-Cristino, 2015 .

Comparison of alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays

M. Ramirez, Francisco R. Pinto, M. Antunes, 2014, BMC Research Notes.

Use of the 13-valent conjugate vaccine has the potential to eliminate pilus carrying isolates as causes of invasive pneumococcal disease.

M. Ramirez, J. Melo-Cristino, S. Aguiar, 2012, Vaccine.

Heterogeneity of pneumococcal phase variants in invasive human infections

M. Ramirez, J. Melo-Cristino, I. Serrano, 2006, BMC Microbiology.

Group A streptococci clones associated with invasive infections and pharyngitis in Portugal present differences in emm types, superantigen gene content and antimicrobial resistance

M. Ramirez, J. Melo-Cristino, Francisco R. Pinto, 2012, BMC Microbiology.

Group B streptococcal infections in infants in Iceland: clinical and microbiological factors

M. Ramirez, Á. Haraldsson, H. Erlendsdóttir, 2021, Journal of medical microbiology.

Group B Streptococcal Neonatal and Early Infancy Infections in Iceland, 1976-2015.

M. Ramirez, K. Kristinsson, J. Melo-Cristino, 2019, The Pediatric infectious disease journal.

Streptococcus agalactiae Causing Neonatal Infections in Portugal (2005–2015): Diversification and Emergence of a CC17/PI-2b Multidrug Resistant Sublineage

M. Ramirez, J. Melo-Cristino, E. Martins, 2017, Front. Microbiol..

Changing epidemiology of group B streptococcal infections among adults in Iceland: 1975-2014.

M. Ramirez, K. Kristinsson, J. Melo-Cristino, 2016, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

Streptococcus agalactiae Serotype Ib as an Agent of Meningitis in Two Adult Nonpregnant Women

M. Ramirez, M. Borrego, L. Brum, 2007, Journal of Clinical Microbiology.

Annotated Whole-Genome Multilocus Sequence Typing Schema for Scalable High-Resolution Typing of Streptococcus pyogenes

M. Ramirez, J. Melo-Cristino, A. Friães, 2022, Journal of clinical microbiology.

Clonal Relationships between Invasive and Noninvasive Lancefield Group C and G Streptococci and emm-Specific Differences in Invasiveness

M. Ramirez, J. Melo-Cristino, M. Pinho, 2006, Journal of Clinical Microbiology.

Clonal Relationships between Invasive and Noninvasive Lanceﬁeld Group C and G Streptococci and emm -Speciﬁc Differences in Invasiveness Streptococcal

M. Ramirez, J. Melo-Cristino, M. Pinho, 2006 .

Population Structure of Streptococcus pneumoniae Causing Invasive Disease in Adults in Portugal before PCV13 Availability for Adults: 2008-2011

M. Ramirez, J. Melo-Cristino, A. Horácio, 2016, PloS one.

Serotyping Streptococcus pneumoniae by Multiplex PCR

M. Ramirez, H. de Lencastre, H. Lencastre, 2003, Journal of Clinical Microbiology.

Clonal and serotype dynamics of serogroup 6 isolates causing invasive pneumococcal disease in Portugal: 1999-2012

João André Carriço, M. Ramirez, J. Melo-Cristino, 2017, PloS one.

Induction of Prophages by Fluoroquinolones in Streptococcus pneumoniae: Implications for Emergence of Resistance in Genetically-Related Clones

M. Ramirez, Ernesto García, J. Liñares, 2014, PloS one.

Streptococcus pneumoniae Serotype 3 in Mexico (1994 to 2017): Decrease of the Unusual Clonal Complex 4909 Lineage following PCV13 Introduction

João André Carriço, Soraia I. Guerreiro, M. Ramirez, 2018, Journal of Clinical Microbiology.

Serotype changes in adult invasive pneumococcal infections in Portugal did not reduce the high fraction of potentially vaccine preventable infections.

M. Ramirez, J. Melo-Cristino, S. Aguiar, 2012, Vaccine.

The Autolysin LytA Contributes to Efficient Bacteriophage Progeny Release in Streptococcus pneumoniae

M. Ramirez, J. Melo-Cristino, M. J. Frias, 2009, Journal of bacteriology.

Expanding the diagnosis of pediatric bacteremic pneumococcal pneumonia from blood cultures to molecular methods: advantages and caveats.

M. Ramirez, J. Melo-Cristino, 2010, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

A Confidence Interval for the Wallace Coefficient of Concordance and Its Application to Microbial Typing Methods

M. Ramirez, J. Melo-Cristino, Francisco R. Pinto, 2008, PloS one.

Identification and characterisation of two transcriptional repressor elements within the coding sequence of the Saccharomyces cerevisiae HXK 2 gene

C. Martínez-Campa, P. Herrero, F. Moreno, 1996 .

Lencastre Multiplex PCR by Streptococcus pneumoniae Serotyping

M. Ramirez, H. Lencastre, D. A. Brito, 2003 .

DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing

Diogo N. Silva, João André Carriço, J. Rossen, 2020, Microbial genomics.

The Majority of Adult Pneumococcal Invasive Infections in Portugal Are Still Potentially Vaccine Preventable in Spite of Significant Declines of Serotypes 1 and 5

M. Ramirez, J. Melo-Cristino, S. Aguiar, 2013, PloS one.

The Viriato Study: update of antimicrobial susceptibility data of bacterial pathogens from community-acquired respiratory tract infections in Portugal in 2003 and 2004.

M. Ramirez, L. Santos, J. Melo-Cristino, 2006, Revista portuguesa de pneumologia.

Continued Vaccine Breakthrough Cases of Serotype 3 Complicated Pneumonia in Vaccinated Children, Portugal (2016–2019)

M. Ramirez, J. Melo-Cristino, A. Friães, 2022, Microbiology spectrum.

Multilocus Sequence Analysis of Streptococcus canis Confirms the Zoonotic Origin of Human Infections and Reveals Genetic Exchange with Streptococcus dysgalactiae subsp. equisimilis

L. Wieler, A. Lübke-Becker, S. Preziuso, 2013, Journal of Clinical Microbiology.

Streptococcus canis Are a Single Population Infecting Multiple Animal Hosts Despite the Diversity of the Universally Present M-Like Protein SCM

T. Kuiken, M. Ramirez, C. Pomba, 2019, Front. Microbiol..

Comparing Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry and Phenotypic and Molecular Methods for Identification of Species within the Streptococcus anginosus Group

João André Carriço, M. Ramirez, J. Melo-Cristino, 2015, Journal of Clinical Microbiology.

First case of infection with vancomycin-resistant Staphylococcus aureus in Europe

M. Ramirez, J. Melo-Cristino, C. Resina, 2013, The Lancet.

Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach

Alexandre P. Francisco, João A. Carriço, Miguel Bugalho, 2009, BMC Bioinformatics.

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

João André Carriço, E. Cercenado, M. Ramirez, 2020, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

Optimal control and analysis of two-color genomotyping experiments using bacterial multistrain arrays

Mário Ramirez, M. Ramirez, J. Melo-Cristino, 2008, BMC Genomics.

Epidemiological Surveillance and Typing Methods to Track Antibiotic Resistant Strains Using High Throughput Sequencing.

Mickael Silva, Mário Ramirez, Bruno Ribeiro-Gonçalves, 2017, Methods in molecular biology.

PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees

Alexandre P. Francisco, Cátia Vaz, João A. Carriço, 2016, Nucleic Acids Res..

Persistence of a single clone of Streptococcus agalactiae causing disease in tilapia (Oreochromis sp.) cultured in Colombia over 8 years.

M. Ramirez, J. Melo-Cristino, C. Iregui, 2015, Journal of fish diseases.

Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas

Mickael Silva, Mário Ramirez, João A Carriço, 2020, Nucleic Acids Res..

Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images

João A. Carriço, Luis Pedro Coelho, Luís Pedro Coelho, 2015, Bioinform..

DEN-IM: Dengue Virus identification from shotgun and targeted metagenomics

João A. Carriço, Mário Ramirez, Natacha Couto, 2019, bioRxiv.

A widespread family of polymorphic toxins encoded by temperate phages

M. Touchon, E. Rocha, João André Carriço, 2017, BMC Biology.

A primer on microbial bioinformatics for nonbioinformaticians.

J A Carriço, M Rossi, J Moran-Gilad, 2018, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

chewBBACA: A complete suite for gene-by-gene schema creation and strain identification

Mirko Rossi, Mickael Silva, Mario Ramirez, 2017, bioRxiv.

Genomic Analysis Reveals the Molecular Basis for Capsule Loss in the Group B Streptococcus Population

H. Tettelin, C. Donati, I. Margarit, 2015, PloS one.

Population Genetics of Streptococcus dysgalactiae Subspecies equisimilis Reveals Widely Dispersed Clones and Extensive Recombination

D. Bessen, M. Ramirez, D. McMillan, 2010, PloS one.

Group A streptococci clones associated with invasive infections and pharyngitis in Portugal present differences in emm types, superantigen gene content and antimicrobial resistance

M. Ramirez, J. Melo-Cristino, A. Friães, 2012, BMC Microbiology.

Consequences of the variability of the CovRS and RopB regulators among Streptococcus pyogenes causing human infections

M. Ramirez, J. Melo-Cristino, A. Friães, 2015, Scientific Reports.

Prophage Spontaneous Activation Promotes DNA Release Enhancing Biofilm Formation in Streptococcus pneumoniae

M. Ramirez, J. Melo-Cristino, M. Carrolo, 2010, PloS one.

Analysis of Typing Methods for Epidemiological Surveillance of both Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Strains

João André Carriço, M. Ramirez, H. de Lencastre, 2007, Journal of Clinical Microbiology.

An Ontology and a REST API for Sequence Based Microbial Typing Data

Alexandre P. Francisco, Cátia Vaz, João A. Carriço, 2010, JBI.

Dominance of Serotype Ia among Group B Streptococci Causing Invasive Infections in Nonpregnant Adults in Portugal

M. Ramirez, J. Melo-Cristino, E. Martins, 2012, Journal of Clinical Microbiology.

Group B Streptococci Causing Neonatal Infections in Barcelona Are a Stable Clonal Population: 18-Year Surveillance

M. Ramirez, A. Andreu, J. Melo-Cristino, 2011, Journal of Clinical Microbiology.

PCR based differentiation between Streptococcus dysgalactiae subsp. equisimilis strains isolated from humans and horses.

E. Acke, S. Preziuso, M. Ramirez, 2014, Comparative immunology, microbiology and infectious diseases.

Prevalence and Drug-Resistance Patterns of Enterotoxigenic Escherichia coli and Shigella Species among Children with Diarrhea in Merida City, Mexico

M. Ramirez, Ana P. Martínez, J. Torres, 2018 .

Invasive infections due to Streptococcus pyogenes: seasonal variation of severity and clinical characteristics, Iceland, 1975 to 2012.

M. Ramirez, D. Weinberger, K. Kristinsson, 2014, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

Emergence of optochin resistance among Streptococcus pneumoniae in Portugal.

M. Ramirez, L. Santos, J. Melo-Cristino, 2007, Microbial drug resistance.

Host lung microbiota promotes malaria-associated acute respiratory distress syndrome

M. Mota, M. Veldhoen, D. Mukherjee, 2022, Nature Communications.

Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data

João A. Carriço, Valeria Bortolaia, Mário Ramirez, 2018, Nucleic Acids Res..

Chapter 86 – Streptococcus pneumoniae

M. Ramirez, Mário Ramirez, 2015 .

LMAS: evaluating metagenomic short de novo assembly methods through defined communities

J. Moran-Gilad, M. Ramirez, J. A. Carriço, 2022, GigaScience.

Changes in Streptococcus pneumoniae serotypes causing invasive disease with non-universal vaccination coverage of the seven-valent conjugate vaccine.

M. Ramirez, J. Melo-Cristino, S. Aguiar, 2008, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

Invasive Pneumococcal Disease in Adults in Portugal: The Importance of Serotypes 8 and 3 (2015–2018)

M. Ramirez, J. Melo-Cristino, C. Silva-Costa, 2021, Microorganisms.

Evaluation of Jackknife and Bootstrap for Defining Confidence Intervals for Pairwise Agreement Measures

João A. Carriço, Mário Ramirez, João André Carriço, 2011, PloS one.

Illustration of a Common Framework for Relating Multiple Typing Methods by Application to Macrolide-Resistant Streptococcus pyogenes

J A Carriço, M Ramirez, João André Carriço, 2006, Journal of Clinical Microbiology.

Emergence of the Same Successful Clade among Distinct Populations of emm89 Streptococcus pyogenes in Multiple Geographic Regions

João Carriço, Catarina Pato, João André Carriço, 2015, mBio.

Serotypes 1, 7F and 19A became the leading causes of pediatric invasive pneumococcal infections in Portugal after 7 years of heptavalent conjugate vaccine use.

M. Ramirez, M. Brito, J. Melo-Cristino, 2010, Vaccine.

Denmark14-230 Clone as an Increasing Cause of Pneumococcal Infection in Portugal within a Background of Diverse Serotype 19A Lineages

M. Ramirez, H. de Lencastre, R. Sá-Leão, 2009, Journal of Clinical Microbiology.