title: Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis.
abstract: Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and Streptococcus pyogenes (group A Streptococcus). For pneumococcus we identified 5,199 putative epistatic interactions between 1,936 sites. Over three-quarters of the links were between sites within the pbp2x, pbp1a and pbp2b genes, the sequences of which are critical in determining non-susceptibility to beta-lactam antibiotics. A network-based analysis found these genes were also coupled to that encoding dihydrofolate reductase, changes to which underlie trimethoprim resistance. Distinct from these antibiotic resistance genes, a large network component of 384 protein coding sequences encompassed many genes critical in basic cellular functions, while another distinct component included genes associated with virulence. The group A Streptococcus (GAS) data set population represents a clonal population with relatively little genetic variation and a high level of linkage disequilibrium across the genome. Despite this, we were able to pinpoint two RNA pseudouridine synthases, which were each strongly linked to a separate set of loci across the chromosome, representing biologically plausible targets of co-selection. The population genomic analysis method applied here identifies statistically significantly co-evolving locus pairs, potentially arising from fitness selection interdependence reflecting underlying protein-protein interactions, or genes whose product activities contribute to the same phenotype. This discovery approach greatly enhances the future potential of epistasis analysis for systems biology, and can complement genome-wide association studies as a means of formulating hypotheses for targeted experimental work.
authors.affiliation: Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America.
authors.forename: Marcin J
authors.identifier: 0000-0002-2022-6766
authors.initials: MJ
authors.lastname: Skwark
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.
authors.forename: Nicholas J
authors.identifier: 0000-0001-6303-8768
authors.initials: NJ
authors.lastname: Croucher
authors.affiliation: Department of Computer Science, Aalto University, Espoo, Finland.
authors.forename: Santeri
authors.identifier: 0000-0001-6388-7110
authors.initials: S
authors.lastname: Puranen
authors.affiliation: Department of Medicine, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Claire
authors.identifier: 0000-0002-1313-4011
authors.initials: C
authors.lastname: Chewapreecha
authors.affiliation: Department of Computer Science, Aalto University, Espoo, Finland.
authors.forename: Maiju
authors.initials: M
authors.lastname: Pesonen
authors.affiliation: Department of Computer Science, Aalto University, Espoo, Finland.
authors.forename: Ying Ying
authors.identifier: 0000-0002-9096-0552
authors.initials: YY
authors.lastname: Xu
authors.affiliation: Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.|Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
authors.forename: Paul
authors.identifier: 0000-0002-1013-7815
authors.initials: P
authors.lastname: Turner
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Simon R
authors.identifier: 0000-0003-1512-6194
authors.initials: SR
authors.lastname: Harris
authors.affiliation: Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, Texas, United States of America.
authors.forename: Stephen B
authors.identifier: 0000-0003-3041-0185
authors.initials: SB
authors.lastname: Beres
authors.affiliation: Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, Texas, United States of America.|Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America.
authors.forename: James M
authors.initials: JM
authors.lastname: Musser
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Julian
authors.identifier: 0000-0002-7069-5958
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.affiliation: Department of Computational Biology, KTH-Royal Institute of Technology, Stockholm, Sweden.|Departments of Applied Physics and Computer Science, Aalto University, Espoo, Finland.|Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Erik
authors.initials: E
authors.lastname: Aurell
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom.|Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.|Department of Biostatistics, University of Oslo, Oslo, Norway.|Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Jukka
authors.initials: J
authors.lastname: Corander
mesh_terms: D019881:Aminoacyltransferases / Q000235:genetics; D000900:Anti-Bacterial Agents / Q000627:therapeutic use; D001426:Bacterial Proteins / Q000235:genetics; D004843:Epistasis, Genetic; D053263:Gene Regulatory Networks / Q000235:genetics; D005828:Genetics, Population; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics; D005838:Genotype; D006801:Humans; D008826:Microbial Sensitivity Tests; D046915:Penicillin-Binding Proteins / Q000737:chemistry / Q000235:genetics; D010458:Peptidyl Transferases / Q000235:genetics; D012641:Selection, Genetic / Q000235:genetics*; D013296:Streptococcus pneumoniae / Q000187:drug effects / Q000235:genetics* / Q000472:pathogenicity; D013297:Streptococcus pyogenes / Q000187:drug effects / Q000235:genetics* / Q000472:pathogenicity; D018440:beta-Lactam Resistance / Q000235:genetics*; D047090:beta-Lactams / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D046915:Penicillin-Binding Proteins; D047090:beta-Lactams; C072223:PBP 2x protein, Streptococcus; D019881:Aminoacyltransferases; C478701:penicillin-binding protein 2b, Streptococcus; C480727:PBP1a protein, Streptococcus pneumoniae; D010458:Peptidyl Transferases