title: Genome-scale analysis of the non-cultivable Treponema pallidum reveals extensive within-patient genetic variation.
abstract: Insights into the genomic adaptive traits of Treponema pallidum, the causative bacterium of syphilis, have long been hampered due to the absence of in vitro culture models and the constraints associated with its propagation in rabbits. Here, we have bypassed the culture bottleneck by means of a targeted strategy never applied to uncultivable bacterial human pathogens to directly capture whole-genome T. pallidum data in the context of human infection. This strategy has unveiled a scenario of discreet T. pallidum interstrain single-nucleotide-polymorphism-based microevolution, contrasting with a rampant within-patient genetic heterogeneity mainly targeting multiple phase-variable loci and a major antigen-coding gene (tprK). TprK demonstrated remarkable variability and redundancy, intra- and interpatient, suggesting ongoing parallel adaptive diversification during human infection. Some bacterial functions (for example, flagella- and chemotaxis-associated) were systematically targeted by both inter- and intrastrain single nucleotide polymorphisms, as well as by ongoing within-patient phase variation events. Finally, patient-derived genomes possess mutations targeting a penicillin-binding protein coding gene (mrcA) that had never been reported, unveiling it as a candidate target to investigate the impact on the susceptibility to penicillin. Our findings decode the major genetic mechanisms by which T. pallidum promotes immune evasion and survival, and demonstrate the exceptional power of characterizing evolving pathogen subpopulations during human infection.
authors.affiliation: Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.|Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
authors.forename: Miguel
authors.initials: M
authors.lastname: Pinto
authors.affiliation: Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.|Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
authors.forename: Vítor
authors.initials: V
authors.lastname: Borges
authors.affiliation: Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
authors.forename: Minia
authors.initials: M
authors.lastname: Antelo
authors.affiliation: School of Medicine, University of St Andrews, KY16 9TF, UK.
authors.forename: Miguel
authors.initials: M
authors.lastname: Pinheiro
authors.affiliation: Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.|Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Nunes
authors.affiliation: Sexually Transmitted Diseases Clinic, Lapa Health Centre, 1200-831 Lisbon, Portugal.
authors.forename: Jacinta
authors.initials: J
authors.lastname: Azevedo
authors.affiliation: Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
authors.forename: Maria José
authors.initials: MJ
authors.lastname: Borrego
authors.affiliation: Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, 1649-016 Lisbon, Portugal.
authors.forename: Joana
authors.initials: J
authors.lastname: Mendonça
authors.affiliation: Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, 1649-016 Lisbon, Portugal.
authors.forename: Dina
authors.initials: D
authors.lastname: Carpinteiro
authors.affiliation: Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, 1649-016 Lisbon, Portugal.
authors.forename: Luís
authors.initials: L
authors.lastname: Vieira
authors.affiliation: Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.|Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal.
authors.forename: João Paulo
authors.initials: JP
authors.lastname: Gomes
mesh_terms: D019143:Evolution, Molecular; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D013587:Syphilis / Q000382:microbiology*; D014210:Treponema pallidum / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification