Chlamydiaceae Genomics Reveals Interspecies Admixture and the Recent Evolution of Chlamydia abortus Infecting Lower Mammalian Species and Humans.
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.
Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine.
Sandeep J
SJ
Joseph
Center for Immunobiology and Vaccine Development, Children's Hospital Oakland Research Institute, Oakland, California.
Hanna
H
Marti
Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom.
Xavier
X
Didelot
Programa de Genomica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
Santiago
S
Castillo-Ramirez
Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine Department of Human Genetics, Emory University School of Medicine.
Timothy D
TD
Read
Center for Immunobiology and Vaccine Development, Children's Hospital Oakland Research Institute, Oakland, California Department of Medicine, University of California, San Francisco Joint Graduate Program in Bioengineering, University of California, San Francisco, and University of California, Berkeley ddean@chori.org.
Deborah
D
Dean
D000818:Animals; D001499:Bayes Theorem; D005075:Biological Evolution; D001717:Birds / Q000382:microbiology; D002689:Chlamydia / Q000235:genetics*; D002691:Chlamydophila psittaci / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D005260:Female; D016680:Genome, Bacterial; D006801:Humans; D008322:Mammals / Q000382:microbiology; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial
Chlamydiaceae; comparative genomics; homologous recombination; molecular clock; population structure; red-tailed hawk