title: Evidence for the evolutionary steps leading to mecA-mediated β-lactam resistance in staphylococci.
abstract: The epidemiologically most important mechanism of antibiotic resistance in Staphylococcus aureus is associated with mecA-an acquired gene encoding an extra penicillin-binding protein (PBP2a) with low affinity to virtually all β-lactams. The introduction of mecA into the S. aureus chromosome has led to the emergence of methicillin-resistant S. aureus (MRSA) pandemics, responsible for high rates of mortality worldwide. Nonetheless, little is known regarding the origin and evolution of mecA. Different mecA homologues have been identified in species belonging to the Staphylococcus sciuri group representing the most primitive staphylococci. In this study we aimed to identify evolutionary steps linking these mecA precursors to the β-lactam resistance gene mecA and the resistance phenotype. We sequenced genomes of 106 S. sciuri, S. vitulinus and S. fleurettii strains and determined their oxacillin susceptibility profiles. Single-nucleotide polymorphism (SNP) analysis of the core genome was performed to assess the genetic relatedness of the isolates. Phylogenetic analysis of the mecA gene homologues and promoters was achieved through nucleotide/amino acid sequence alignments and mutation rates were estimated using a Bayesian analysis. Furthermore, the predicted structure of mecA homologue-encoded PBPs of oxacillin-susceptible and -resistant strains were compared. We showed for the first time that oxacillin resistance in the S. sciuri group has emerged multiple times and by a variety of different mechanisms. Development of resistance occurred through several steps including structural diversification of the non-binding domain of native PBPs; changes in the promoters of mecA homologues; acquisition of SCCmec and adaptation of the bacterial genetic background. Moreover, our results suggest that it was exposure to β-lactams in human-created environments that has driven evolution of native PBPs towards a resistance determinant. The evolution of β-lactam resistance in staphylococci highlights the numerous resources available to bacteria to adapt to the selective pressure of antibiotics.
authors.affiliation: Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal.|Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal.
authors.forename: Joana
authors.identifier: 0000-0002-5291-212X
authors.initials: J
authors.lastname: Rolo
authors.affiliation: MRSA Knowledge Center, Department of Clinical Microbiology, Hvidovre Hospital, Hvidovre, Denmark.
authors.forename: Peder
authors.initials: P
authors.lastname: Worning
authors.affiliation: MRSA Knowledge Center, Department of Clinical Microbiology, Hvidovre Hospital, Hvidovre, Denmark.
authors.forename: Jesper
authors.initials: J
authors.lastname: Boye Nielsen
authors.affiliation: UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.
authors.forename: Rita
authors.identifier: 0000-0003-4533-7531
authors.initials: R
authors.lastname: Sobral
authors.affiliation: Department of Statistics, University of Oxford, Oxford, United Kingdom.
authors.forename: Rory
authors.initials: R
authors.lastname: Bowden
authors.affiliation: Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal.|Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal.
authors.forename: Ons
authors.initials: O
authors.lastname: Bouchami
authors.affiliation: Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Peter
authors.initials: P
authors.lastname: Damborg
authors.affiliation: Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.|Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, St Kitts, West Indies.
authors.forename: Luca
authors.initials: L
authors.lastname: Guardabassi
authors.affiliation: Department of Molecular Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
authors.forename: Vincent
authors.identifier: 0000-0001-5722-9445
authors.initials: V
authors.lastname: Perreten
authors.affiliation: MRSA Knowledge Center, Department of Clinical Microbiology, Hvidovre Hospital, Hvidovre, Denmark.|Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Henrik
authors.initials: H
authors.lastname: Westh
authors.affiliation: Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, United States of America.
authors.forename: Alexander
authors.initials: A
authors.lastname: Tomasz
authors.affiliation: Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal.|Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, United States of America.
authors.forename: Hermínia
authors.initials: H
authors.lastname: de Lencastre
authors.affiliation: Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal.|Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal.
authors.forename: Maria
authors.identifier: 0000-0002-1323-7184
authors.initials: M
authors.lastname: Miragaia
mesh_terms: D000900:Anti-Bacterial Agents / Q000627:therapeutic use; D001426:Bacterial Proteins / Q000235:genetics*; D001499:Bayes Theorem; D006801:Humans; D055624:Methicillin-Resistant Staphylococcus aureus / Q000187:drug effects / Q000235:genetics; D046915:Penicillin-Binding Proteins / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D013203:Staphylococcal Infections / Q000188:drug therapy / Q000235:genetics*; D013210:Staphylococcus / Q000187:drug effects / Q000235:genetics*; D018440:beta-Lactam Resistance / Q000235:genetics*; D047090:beta-Lactams / Q000627:therapeutic use
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D046915:Penicillin-Binding Proteins; D047090:beta-Lactams; C487789:mecA protein, Staphylococcus aureus