The Info List - Chlamydiae

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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.[1] 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.[2][3][4] 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.[5][6][7] 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.


1 History 2 Nomenclature 3 Taxonomy and molecular signatures 4 Phylogenetics 5 Human pathogens and diagnostics 6 Phylogeny 7 Taxonomy 8 References 9 External links

History[edit] 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
Chlamydia trachomatis
was first cultured by Tang Fei-fan, though they were not yet recognized as bacteria.[8] Nomenclature[edit] In 1966, Chlamydiae
were recognized as bacteria and the genus Chlamydia
was validated.[9] The order Chlamydiales was created by Storz and Page in 1971. The class Chlamydiia
was recently validly published.[10][11][12] Between 1989 and 1999, new families, genera, and species were recognized. The phylum Chlamydiae
was established in Bergey's Manual of Systematic Bacteriology.[13] By 2006, genetic data for over 350 chlamydial lineages had been reported,[14] Taxonomy and molecular signatures[edit] The Chlamydiae
currently contain eight validly named genera, and 14 candidatus genera.[15] The phylum presently consist of two orders (Chlamydiales, Parachlamydiales) and nine families within a single class (Chlamydiia).[10][11] Only four of these families are validly named (Chlamydiaceae, Parachlamydiaceae, Simkaniaceae, Waddliaceae)[16][17] while five are described as Candidatus families (Clavichlamydiaceae, Criblamydiaceae, Parilichlamydiaceae, Piscichlamydiaceae, and Rhabdochlamydiaceae).[18][19][20] The Chlamydiales order as recently described contains the families Chlamydiaceae, and the Candidatus Clanchiamydiaceae, while the new Parachlamydiales order harbors the remaining seven families.[10] 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.[10][21] 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 Chlamydiaceae family.[10][21] The Chlamydiaceae originally consisted of two genera, Chlamydophila and Chlamydia. The genera have been recently united where species belonging to the Chlamydophila genus have been reclassified as Chlamydia
species.[22][23] 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.[10][21] 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. Phylogenetics[edit] 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.[10][21][24][25] 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.[26][27] Reports have varied as to whether the Chlamydiae
are related to the Planctomycetales or Spirochaetes.[28][29] 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.[25] 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.[30] Comparison of ribosomal RNA genes has provided a phylogeny of known strains within Chlamydiae.[14] Human pathogens and diagnostics[edit] Three species of Chlamydiae
that commonly infect humans are described:

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.[31] 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. Phylogeny[edit] See also: Bacterial
taxonomy The phylogeny is based on 16S rRNA-based LTP release 123 by The All-Species Living Tree Project.[32]


Waddlia chondrophila Rurangirwa et al. 1999


Simkania negevensis Everett, Bush & Andersen 1999


Neochlamydia hartmannellae Horn et al. 2001

Parachlamydia acanthamoebae Everett, Bush & Andersen 1999


Chlamydophila pneumoniae (Grayston et al. 1989) Everett, Bush & Andersen 1999


C. felis Everett, Bush & Andersen 1999

C. psittaci (Lillie 1930) Everett, Bush & Andersen 1999

C. caviae Everett, Bush & Andersen 1999

C. abortus Everett, Bush & Andersen 1999


C. pecorum Fukushi and Hirai 1992

C. muridarum Everett, Bush & Andersen 1999

C. suis Everett, Bush & Andersen 1999

C. trachomatis (Busacca 1935) Rake 1957 emend. Everett, Bush & Andersen 1999

Notes: ♠ 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) Taxonomy[edit] The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[33] and the NCBI[34]

Genus ?"Candidatus Piscichlamydia" ♠ Draghi et al. 2004

Species "Candidatus Piscichlamydia salmonis" ♠ Draghi et al. 2004

Family ?"Candidatus Actinochlamydiaceae" ♠ Steigen et al. 2013

Genus "Candidatus Actinochlamydia" ♠ Steigen et al. 2013

Species "Candidatus Actinochlamydia clariae" ♠ Steigen et al. 2013

Family ?"Candidatus Clavichlamydiaceae" ♠ Horn 2011

Genus "Candidatus Clavichlamydia" ♠ corrig. Karlsen et al. 2008

Species "Candidatus Clavichlamydia salmonicola" ♠ corrig. Karlsen et al. 2008

Family ?"Candidatus Parilichlamydiaceae" ♠ Stride et al. 2013

Genus "Candidatus Parilichlamydia" ♠ Stride et al. 2013

Species "Candidatus Parilichlamydia carangidicola" ♠ Stride et al. 2013

Genus "Candidatus Similichlamydia" ♠ Stride et al. 2013

Species " Ca. S. latridicola" ♠ Stride et al. 2013 Species " Ca. S. labri" ♠ Steigen et al. 2015

Family Criblamydiaceae ♠ Thomas, Casson & Greub 2006

"Criblamydia" ♠ Thomas, Casson & Greub 2006

Species "Criblamydia sequanensis" ♠ Thomas, Casson & Greub 2006

"Estrella" ♠ Thomas et al. 2006

Species "Estrella lausannensis" ♠ Corsaro, Feroldi & Greub 2007

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

Species "Ca. R. crassificans" ♠ Corsaro et al. 2007 ["Rickettsiella crassificans" Radek 2000] Species "Ca. R. porcellionis" ♠ Kostanjsek et al. 2004 ["Chlamydia isopodii" Shay et al. 1985]

Family Chlamydiaceae Rake 1957 emend. Everett, Bush & Andersen 1999

Genus "Candidatus Amphibiichlamydia" ♠ Martel et al. 2012

Species "Ca. A. ranarum" ♠ Martel et al. 2013 Species "Ca. A. salamandrae" ♠ 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

Species "Candidatus P. amoebophila" Collingro et al. 2005 Species "P. naegleriophila" ♠ Casson et al. 2006

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]

Family Simkaniaceae Everett, Bush & Andersen 1999

Genus ?"Candidatus Fritschea" Everett et al. 2005

Species "Candidatus F. bemisiae" Everett et al. 2005 Species "Candidatus F. eriococci" 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

Species "Ca. S. salmonis" ♠ Nylund et al. 2015 Species "Ca. S. venezia" ♠ Fehr et al. 2013

Genus Simkania Everett, Bush & Andersen 1999

Species Simkania negevensis Everett, Bush & Andersen 1999

Family Waddliaceae Rurangirwa et al. 1999

Genus Waddlia Rurangirwa et al. 1999

Species W. chondrophila Rurangirwa et al. 1999 Species "W. malaysiensis" ♥ Chua et al. 2005


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External links[edit]

Chlamydiae.com, a comprehensive information source from Dr. Michael Ward (Professor of Medical Microbiology in the University of Southampton)

v t e

Prokaryotes: Bacteria
classification (phyla and orders)

Domain Archaea Bacteria Eukaryota (Supergroup Plant Hacrobia Heterokont Alveolata Rhizaria Excavata Amoebozoa Opisthokonta

Animal Fungi)

G-/ OM

Terra-/ Glidobacteria (BV1)



Deinococcales Thermales


Anaerolineales Caldilineales Chloroflexales Herpetosiphonales Dehalococcoidales Ktedonobacterales Thermogemmatisporales Thermomicrobiales Sphaerobacterales

other glidobacteria

Thermodesulfobacteria thermophiles

Aquificae Thermotogae


Proteobacteria (BV2)


Caulobacterales Kiloniellales Kordiimonadales Magnetococcales Parvularculales Rhizobiales Rhodobacterales Rhodospirillales Rickettsiales Sneathiellales Sphingomonadales


Burkholderiales Hydrogenophilales Methylophilales Neisseriales Nitrosomonadales Procabacteriales Rhodocyclales


Acidithiobacillales Aeromonadales Alteromonadales Cardiobacteriales Chromatiales Enterobacteriales Legionellales Methylococcales Oceanospirillales Orbales Pasteurellales Pseudomonadales Salinisphaerales Thiotrichales Vibrionales Xanthomonadales


Bdellovibrionales Desulfarculales Desulfobacterales Desulfovibrionales Desulfurellales Desulfuromonadales Myxococcales Syntrophobacterales Syntrophorhabdales


Campylobacterales Nautiliales






Sphingobacteria (FCB group)

Fibrobacteres Chlorobi

Chlorobiales Ignavibacteriales


Bacteroidales Cytophagales Flavobacteriales Sphingobacteriales

Planctobacteria/ (PVC group)

Chlamydiae Lentisphaerae

Lentisphaerales Oligosphaerales Victivallales


Phycisphaerales Planctomycetales


Puniceicoccales Opitutales Chthoniobacterales Verrucomicrobiales


Other GN


Acidobacteriales Acanthopleuribacterales Holophagales Solibacterales


Armatimonadales Chthonomonadales Fimbriimonadales

Caldiserica Chrysiogenetes Deferribacteres Dictyoglomi Elusimicrobia Fusobacteria Gemmatimonadetes Nitrospirae Synergistetes

G+/ no OM

Firmicutes (BV3)


Bacillales Lactobacillales


Clostridiales Halanaerobiales Thermoanaerobacteriales Natranaerobiales





Tenericutes/ Mollicutes

Mycoplasmatales Entomoplasmatales Anaeroplasmatales Acholeplasmatales Haloplasmatales



Actinobacteria (BV5)


Actinomycetales Bifidobacteriales






Euzebyales Nitriliruptorales


Gaiellales Rubrobacterales Thermoleophilales Solirubrobacterales

Incertae sedis

†Archaeosphaeroides †Eobacterium †Leptotrichites

Source: Bergey's Manual (2001–2012). Alternative views: Wikispecies.

v t e

Infectious diseases Bacterial
diseases: BV4 non-proteobacterial G- (primarily A00–A79, 001–041, 080–109)





Syphilis/bejel Yaws

carateum (Pinta) Treponema


burgdorferi/ Borrelia

Lyme disease Erythema chronicum migrans Neuroborreliosis

recurrentis (Louse borne relapsing fever) Borrelia
hermsii/ Borrelia
duttoni/ Borrelia
parkeri (Tick borne relapsing fever)



interrogans (Leptospirosis)



Chlamydophila psittaci (Psittacosis) Chlamydophila pneumoniae



Chlamydia Lymphogranuloma venereum Trachoma


Bacteroides fragilis Tannerella forsythia Capnocytophaga canimorsus Porphyromonas gingivalis Prevotella intermedia


Fusobacterium necrophorum (Lemierre's syndrome) Fusobacterium nucleatum Fusobacterium polymorphum

Streptobacillus moniliformis (Rat-bite fever/Haverhill fever)


Taxon identifiers

Wd: Q875679 EoL: 7829 EPPO: 1CHLMC GBIF: 82 ITIS: 9