title: Population structure and minimum core genome typing of Legionella pneumophila.
abstract: Legionella pneumophila is an important human pathogen causing Legionnaires' disease. In this study, whole genome sequencing (WGS) was used to study the characteristics and population structure of L. pneumophila strains. We sequenced and compared 53 isolates of L. pneumophila covering different serogroups and sequence-based typing (SBT) types (STs). We found that 1,896 single-copy orthologous genes were shared by all isolates and were defined as the minimum core genome (MCG) of L. pneumophila. A total of 323,224 single-nucleotide polymorphisms (SNPs) were identified among the 53 strains. After excluding 314,059 SNPs which were likely to be results of recombination, the remaining 9,165 SNPs were referred to as MCG SNPs. Population Structure analysis based on MCG divided the 53 L. pneumophila into nine MCG groups. The within-group distances were much smaller than the between-group distances, indicating considerable divergence between MCG groups. MCG groups were also supplied by phylogenetic analysis and may be considered as robust taxonomic units within L. pneumophila. Among the nine MCG groups, eight showed high intracellular growth ability while one showed low intracellular growth ability. Furthermore, MCG typing also showed high resolution in subtyping ST1 strains. The results obtained in this study provided significant insights into the evolution, population structure and pathogenicity of L. pneumophila.
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention. Beijing, 102206, China.|Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China.
authors.forename: Tian
authors.initials: T
authors.lastname: Qin
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention. Beijing, 102206, China.|Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Novogene Bioinformatics Technology Co. Ltd, Beijing, 100083, China.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Liu
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention. Beijing, 102206, China.|Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China.
authors.forename: Haijian
authors.initials: H
authors.lastname: Zhou
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention. Beijing, 102206, China.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Ren
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention. Beijing, 102206, China.|Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China.
authors.forename: Zhujun
authors.initials: Z
authors.lastname: Shao
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
authors.forename: Ruiting
authors.initials: R
authors.lastname: Lan
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention. Beijing, 102206, China.|Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China.
authors.forename: Jianguo
authors.initials: J
authors.lastname: Xu
mesh_terms: D030541:Databases, Genetic; D056426:Genetic Loci; D016680:Genome, Bacterial; D005838:Genotype; D060005:Genotyping Techniques; D006801:Humans; D016952:Legionella pneumophila / Q000235:genetics*