Garrity & Holt 2012
Gupta et al. 2016
|Orders and families|
The Chlamydiae are bacterial phylum and class whose members are a group of obligate intracellular bacteria, whose members are remarkably diverse, ranging from pathogens of humans and animals to symbionts of ubiquitous protozoa. They are ovoid in shape and stain Gram-negative. Historically it was believed that all Chlamydiae species had a peptidoglycan-free cell wall, but recent work demonstrates a detectable presence of peptidoglycan, as well as other important proteins. Many species belonging to this order are susceptible to antimicrobial agents. All known Chlamydiae only grow by infecting eukaryotic host cells, they are as small as or smaller than many viruses. They are dependent on replication inside the host cells, thus some species are termed obligate intracellular pathogens and others are symbionts of ubiquitous protozoa. Most intracellular Chlamydiae are located in an inclusion body or vacuole. Outside cells, they survive only as an extracellular infectious form. Chlamydiae can grow only where their host cells grow, and develop according to a characteristic biphasic developmental cycle. Therefore, Chlamydiae cannot be propagated in bacterial culture media in the clinical laboratory. Chlamydiae are most successfully isolated while still inside their host cells. Chlamydiae is the most common bacterial STD in the United States and 2.86 million chlamydiae infections are reported annually.
Chlamydia-like disease affecting the eyes of people was first described in ancient Chinese and Egyptian manuscripts. A modern description of chlamydia-like organisms was provided by Halberstaedrrter and von Prowazek in 1907. Chlamydial isolates cultured in the yolk sacs of embryonating eggs were obtained from a human pneumonitis outbreak in the late 1920s and early 1930s, and by the mid-20th century, isolates had been obtained from dozens of vertebrate species; the term 'chlamydia' (a cloak) appeared in the literature in 1945, although other names continued to be used, including Bedsonia, Miyagawanella, ornithosis-, TRIC-, and PLT-agents. In 1956, Chlamydia trachomatis was first cultured by Tang Fei-fan, though they were not yet recognized as bacteria.
In 1966, Chlamydiae were recognized as bacteria and the genus Chlamydia was validated; the order Chlamydiales was created by Storz and Page in 1971. The class Chlamydiia was recently validly published. Between 1989 and 1999, new families, genera, and species were recognized; the phylum Chlamydiae was established in Bergey's Manual of Systematic Bacteriology. By 2006, genetic data for over 350 chlamydial lineages had been reported,
Taxonomy and molecular signatures
The Chlamydiae currently contain eight validly named genera, and 14 candidatus genera; the phylum presently consist of two orders (Chlamydiales, Parachlamydiales) and nine families within a single class (Chlamydiia). Only four of these families are validly named (Chlamydiaceae, Parachlamydiaceae, Simkaniaceae, Waddliaceae) while five are described as Candidatus families (Clavichlamydiaceae, Criblamydiaceae, Parilichlamydiaceae, Piscichlamydiaceae, and Rhabdochlamydiaceae); the Chlamydiales order as recently described contains the families Chlamydiaceae, and the Candidatus Clanchiamydiaceae, while the new Parachlamydiales order harbors the remaining seven families. This proposal is supported by the observation of two distinct phylogenetic clades that warrant taxonomic ranks above the family level. Molecular signatures in the form of conserved indels (CSIs) and proteins (CSPs) have been found to be uniquely shared by each separate order, providing a means of distinguishing each clade from the other and supporting the view of shared ancestry of the families within each order; the distinctness of the two orders is also supported by the fact that no CSIs were found among any other combination of families.
Molecular signatures have also been found that are exclusive for the family Chlamydiaceae; the Chlamydiaceae originally consisted of one genus, Chlamydia, but in 1999 was split into two genera, Chlamydophila and Chlamydia. The genera have since 2015 been reunited where species belonging to the genus Chlamydophila have been reclassified as Chlamydia species. However, CSIs and CSPs have been found specifically for Chlamydophila species, supporting their distinctness from Chlamydia, perhaps warranting additional consideration of two separate groupings within the family. CSIs and CSPs have also been found that are exclusively shared by all Chlamydia that are further indicative of a lineage independent from Chlamydophila, supporting a means to distinguish Chlamydia species from neighbouring Chlamydophila members.
The Chlamydiae form a unique bacterial evolutionary group that separated from other bacteria about a billion years ago, and can be distinguished by the presence of several CSIs and CSPs; the species from this group can be distinguished from all other bacteria by the presence of conserved indels in a number of proteins and by large numbers of signature proteins that are uniquely present in different Chlamydiae species. Reports have varied as to whether the Chlamydiae are related to the Planctomycetales or Spirochaetes. Genome sequencing, however, indicates that 11% of the genes in Candidatus Protochlamydia amoebophila UWE25 and 4% in the Chlamydiaceae are most similar to chloroplast, plant, and cyanobacterial genes. Cavalier-Smith has postulated that the Chlamydiae fall into the clade Planctobacteria in the larger clade Gracilicutes. However, phylogeny and shared presence of CSIs in proteins that are lineage-specific indicate that the Verrucomicrobia are the closest free-living relatives of these parasitic organisms. Comparison of ribosomal RNA genes has provided a phylogeny of known strains within Chlamydiae.
Human pathogens and diagnostics
Three species of Chlamydiae that commonly infect humans are described:
- Chlamydia trachomatis, which causes the eye-disease trachoma and the sexually transmitted infection chlamydia
- Chlamydophila pneumoniae, which causes a form of pneumonia
- Chlamydophila psittaci, which causes psittacosis
The unique physiological status of the Chlamydiae including their biphasic lifecycle and obligation to replicate within a eukaryotic host has enabled the use of DNA analysis for chlamydial diagnostics. Horizontal transfer of genes is evident and complicates this area of research. In one extreme example, two genes encoding histone-like H1 proteins of eukaryotic origin have been found in the prokaryotic genome of C. trachomatis, an obligate intracellular pathogen.
♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LSPN)
♥ Strains not lodged at National Center for Biotechnology Information (NCBI) and or listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN)
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the NCBI
- Genus ?"Candidatus Piscichlamydia" ♠ Draghi et al. 2004
- Species "Candidatus Piscichlamydia salmonis" ♠ Draghi et al. 2004
- Family ?"Candidatus Actinochlamydiaceae" ♠ Steigen et al. 2013
- Family ?"Candidatus Clavichlamydiaceae" ♠ Horn 2011
- Family ?"Candidatus Parilichlamydiaceae" ♠ Stride et al. 2013
- Family Criblamydiaceae ♠ Thomas, Casson & Greub 2006
- Family "Candidatus Rhabdochlamydiaceae" ♠ Corsaro et al. 2009
- Genus "Candidatus Renichlamydia" ♠ Corsaro & Work 2012
- Species "Candidatus Renichlamydia lutjani" ♠ Corsaro & Work 2012
- Genus "Candidatus Rhabdochlamydia" ♠ Kostanjsek et al. 2004
- Genus "Candidatus Renichlamydia" ♠ Corsaro & Work 2012
- Family Chlamydiaceae Rake 1957 emend. Everett, Bush & Andersen 1999
- Genus "Candidatus Amphibiichlamydia" ♠ Martel et al. 2012
- Genus "Candidatus Rubidus" ♠ Pagnier et al. 2015
- Species "Candidatus Rubidus massiliensis" ♠ Pagnier et al. 2015
- Genus Chlamydia Jones et al. 1945 emend. Everett, Bush & Andersen 1999
- Species ?"C. ibidis" ♠ Vorimore et al. 2013
- Species C. avium Sachse et al. 2015 ["Chlamydia avium" Sachse et al. 2014]
- Species C. gallinacea Sachse et al. 2015 ["Chlamydia gallinacea" Sachse et al. 2014]
- Species C. pecorum Fukushi & Hirai 1992 [Chlamydophila pecorum (Fukushi & Hirai 1992) Everett et al. 1999]
- Species C. muridarum Everett, Bush & Andersen 1999 (agent of mouse pneumonitis)
- Species C. suis Everett, Bush & Andersen 1999
- Species C. trachomatis (Busacca 1935) Rake 1957 emend. Everett, Bush & Andersen 1999 ["Rickettsia trachomae" (sic) Busacca 1935; "Rickettsia trachomatis" (Busacca 1935) Foley & Parrot 1937; "Chlamydozoon trachomatis" (Busacca 1935) Moshkovski 1945]
- Species Chlamydia pneumoniae Grayston et al. 1989 [Chlamydophila pneumoniae (Grayston et al. 1989) Everett, Bush & Andersen 1999]
- Genus Chlamydophila Everett, Bush & Andersen 1999
- Species C. felis Everett et al. 1999 ["Chlamydia felis" (Everett, Bush & Andersen 1999) Kuo et al. 2011]
- Species C. psittaci (Lillie 1930) Everett, Bush & Andersen 1999 [Chlamydia psittaci (Lillie 1930) Page 1968; "Rickettsiaformis psittacosis" Zhdanov & Korenblit 1950; "Rickettsia psittaci" Lillie 1930; "Ehrlichia psittaci" (Lillie 1930) Moshkovski 1945; "Chlamydozoon psittaci"" (Lillie 1930) Ryzhkov 1950]
- Species C. abortus Everett, Bush & Andersen 1999 ["Chlamydia abortus" (Everett, Bush & Andersen 1999) Kuo et al. 2011]
- Species C. caviae Everett, Bush & Andersen 1999 ["Chlamydia caviae" (Everett, Bush & Andersen 1999) Kuo et al. 2011]
- Family Parachlamydiaceae Everett, Bush & Andersen 1999
- Genus ?"Candidatus Mesochlamydia" ♠ Corsaro et al. 2012
- Species "Candidatus Mesochlamydia elodeae" ♠ Corsaro et al. 2012
- Genus ?"Candidatus Metachlamydia" ♠ Corsaro et al. 2010
- Species "Candidatus Metachlamydia lacustris" ♠ Corsaro et al. 2010
- Genus ?"Protochlamydia" ♠ Collingro et al. 2005
- Genus Neochlamydia Horn et al. 2001
- Species Neochlamydia hartmannellae Horn et al. 2001 ["Neochlamydia hartmannellae" Horn et al. 2000; "Parachlamydia hartmannellae"]
- Genus Parachlamydia Everett, Bush & Andersen 1999
- Species Parachlamydia acanthamoebae Everett, Bush & Andersen 1999 ["Candidatus Parachlamydia acanthamoebae" Amann et al. 1997]
- Genus ?"Candidatus Mesochlamydia" ♠ Corsaro et al. 2012
- Family Simkaniaceae Everett, Bush & Andersen 1999
- Genus ?"Candidatus Fritschea" Everett et al. 2005
- Genus ?"Candidatus Neptunochlamydia" ♠ Pizzetti et al. 2016
- Species "Candidatus Neptunochlamydia vexilliferae" ♠ Pizzetti et al. 2016
- Genus ?"Candidatus Syngnamydia" ♠ Fehr et al. 2013
- Genus Simkania Everett, Bush & Andersen 1999
- Species Simkania negevensis Everett, Bush & Andersen 1999
- Family Waddliaceae Rurangirwa et al. 1999
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