Chlamydiaceae Genomics Reveals Interspecies Admixture and the Recent Evolution of Chlamydia abortus Infecting Lower Mammalian Species and Humans

• Type of Material: Article
• Authors: Sandeep J. Joseph, Emory University; Hanna Marti, Children’s Hospital Oakland Research Institute; Xavier Didelot, Imperial College London; Santiago Castillo-Ramirez, Universidad Nacional Autónoma de México; Timothy Read, Emory University; Deborah Dean, Children’s Hospital Oakland Research Institute
• Language: English
• Date: 2015-10-27
• Publisher: Oxford University Press (OUP): Policy C - Option B
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2015.
• License: Creative Commons Attribution-NonCommercial 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1093/gbe/evv201
• Title of Journal or Parent Work: Genome Biology and Evolution
• ISSN: 1759-6653
• Volume: 7
• Issue: 11
• Start Page: 3070
• End Page: 3084
• Grant/Funding Information: This work was supported in part by the Public Health Service grant from the National Institute of Health (R01 AI098843 to D.D. and T.D.R.); and the National Science Foundation (NIH) (2009-65109-05760 to D.D.) and an Early Postdoctoral Mobility Fellowship grant from the Swiss National Science Foundation (SNSF) (P2ZHP3_158590 to H.M.).
• Keywords: homologous recombination; RECOMBINATION; population structure; Life Sciences & Biomedicine; TRACHOMATIS STRAINS; Evolutionary Biology; POPULATION-STRUCTURE; PECORUM; Genetics & Heredity; SELECTION; IN-VITRO; red-tailed hawk; molecular clock; CHLAMYDOPHILA-PSITTACI; comparative genomics; SEQUENCE DATA; Science & Technology; FAMILY CHLAMYDIACEAE; SP-NOV; Chlamydiaceae
• Research Categories: Biology, Genetics; Health Sciences, Pathology; Health Sciences, Epidemiology

Abstract

Chlamydiaceae are obligate intracellular bacteria that cause a diversity of severe infections among humans and livestock on a global scale. Identification of new species since 1989 and emergence of zoonotic infections, including abortion in women, underscore the need for genome sequencing of multiple strains of each species to advance our knowledge of evolutionary dynamics across Chlamydiaceae. Here, we genome sequenced isolates from avian, lower mammalian and human hosts. Based on core gene phylogeny, five isolates previously classified as Chlamydia abortus were identified as members of Chlamydia psittaci and Chlamydia pecorum. Chlamydia abortus is the most recently emerged species and is a highly monomorphic group that lacks the conserved virulence-associated plasmid. Low-level recombination and evidence for adaptation to the placenta echo evolutionary processes seen in recently emerged, highly virulent niche-restricted pathogens, such as Bacillus anthracis. In contrast, gene flow occurred within C. psittaci and other Chlamydiaceae species. The C. psittaci strain RTH, isolated from a red-tailed hawk (Buteo jamaicensis), is an outlying strain with admixture of C. abortus, C. psittaci, and its own population markers. An average nucleotide identity of less than 94% compared with other Chlamydiaceae species suggests that RTH belongs to a new species intermediary between C. psittaci and C. abortus. Hawks, as scavengers and predators, have extensive opportunities to acquire multiple species in their intestinal tract. This could facilitate transformation and homologous recombination with the potential for new species emergence. Our findings indicate that incubator hosts such as birds-of-prey likely promote Chlamydiaceae evolution resulting in novel pathogenic lineages.