Chlamydiae

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Chlamydiae
ChlamydiaTrachomatisEinschlusskorperchen.jpg
Chlamydia trachomatis
Scientific classification
Domain:
Bacteria
Superphylum:
PVC group
Phylum:
Chlamydiae

Garrity & Holt 2012
Class:
Chlamydiia

Gupta et al. 2016
Orders and families
Synonyms
  • Chlamydaeota Oren et al. 2015

The Chlamydiae are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, [1] and marine sediment forms not yet well understood. [2] All of the Chlamydiae that humans have known about for many decades are obligate intracellular bacteria; in 2020 many additional Chlamydiae were discovered in ocean-floor environments, and it is not yet known whether they all have hosts. [2] Historically it was believed that all Chlamydiae had a peptidoglycan-free cell wall, but studies in the 2010s demonstrated a detectable presence of peptidoglycan, as well as other important proteins. [3] [4] [5]

Contents

Among the Chlamydiae, all of the ones long known to science grow only by infecting eukaryotic host cells. They are as small as or smaller than many viruses. They are ovoid in shape and stain Gram-negative. 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. These Chlamydiae can grow only where their host cells grow, and develop according to a characteristic biphasic developmental cycle. [6] [7] [8] Therefore, clinically relevant Chlamydiae cannot be propagated in bacterial culture media in the clinical laboratory. They are most successfully isolated while still inside their host cells.

Of various Chlamydiae that cause human disease, the two most important species are Chlamydia pneumoniae , which causes a type of pneumonia, and Chlamydia trachomatis , which causes chlamydia. Chlamydia is the most common bacterial sexually transmitted infection in the United States, and 2.86 million chlamydia infections are reported annually.

History

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. [9]

Nomenclature

In 1966, Chlamydiae were recognized as bacteria and the genus Chlamydia was validated. [10] The order Chlamydiales was created by Storz and Page in 1971. The class Chlamydiia was recently validly published. [11] [12] [13] Between 1989 and 1999, new families, genera, and species were recognized. The phylum Chlamydiae was established in Bergey's Manual of Systematic Bacteriology. [14] By 2006, genetic data for over 350 chlamydial lineages had been reported. [15] Discovery of ocean-floor forms reported in 2020 involves new clades. [2]

Taxonomy and molecular signatures

The Chlamydiae currently contain eight validly named genera, and 14 genera. [16] The phylum presently consist of two orders (Chlamydiales, Parachlamydiales) and nine families within a single class (Chlamydiia). [11] [12] Only four of these families are validly named (Chlamydiaceae, Parachlamydiaceae, Simkaniaceae, Waddliaceae) [17] [18] while five are described as families (Clavichlamydiaceae, Criblamydiaceae, Parilichlamydiaceae, Piscichlamydiaceae, and Rhabdochlamydiaceae). [19] [20] [21] The Chlamydiales order as recently described contains the families Chlamydiaceae, and the Clanchiamydiaceae, while the new Parachlamydiales order harbors the remaining seven families. [11] 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. [11] [22] 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. [11] [22] 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. [23] [24] 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. [11] [22] 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

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. [11] [22] [25] [26] 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. [27] [28] Reports have varied as to whether the Chlamydiae are related to the Planctomycetales or Spirochaetes. [29] [30] Genome sequencing, however, indicates that 11% of the genes in Protochlamydia amoebophila UWE25 and 4% in the Chlamydiaceae are most similar to chloroplast, plant, and cyanobacterial genes. [26] 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. [31] Comparison of ribosomal RNA genes has provided a phylogeny of known strains within Chlamydiae. [15]

Human pathogens and diagnostics

Three species of Chlamydiae that commonly infect humans are described:

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. [32] 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

The phylogeny is based on 16S rRNA-based LTP release 123 by The All-Species Living Tree Project. [33]

 
Waddliaceae

Waddlia chondrophila Rurangirwa et al. 1999

 
 
Simkaniaceae

Simkania negevensis Everett, Bush & Andersen 1999

 
Parachlamydiaceae
 

Neochlamydia hartmannellae Horn et al. 2001

 
 

Parachlamydia acanthamoebae Everett, Bush & Andersen 1999

 
 
 
 
Chlamydiaceae
 

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

 
 
Chlamydophila
 

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

 
 
 
 
Chlamydia
 

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

 
 
 
 
 
 

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [34] and the NCBI [35]

Related Research Articles

Chlamydia Sexually transmitted infection caused by the bacterium Chlamydia trachomatis.

Chlamydia, or more specifically a chlamydia infection, is a sexually transmitted infection caused by the bacterium Chlamydia trachomatis. Most people who are infected have no symptoms. When symptoms do appear they may occur only several weeks after infection; the incubation period between exposure and being able to infect others is thought to be on the order of two to six weeks. Symptoms in women may include vaginal discharge or burning with urination. Symptoms in men may include discharge from the penis, burning with urination, or pain and swelling of one or both testicles. The infection can spread to the upper genital tract in women, causing pelvic inflammatory disease, which may result in future infertility or ectopic pregnancy.

Nanoarchaeota Phylum of archaea

Nanoarchaeota are a phylum of the Archaea. This phylum currently has only one representative, Nanoarchaeum equitans.

<i>Chlamydia trachomatis</i> Species of bacterium

Chlamydia trachomatis, commonly known as chlamydia, is a bacterium that causes chlamydia, which can manifest in various ways, including: trachoma, lymphogranuloma venereum, nongonococcal urethritis, cervicitis, salpingitis, pelvic inflammatory disease. C. trachomatis is the most common infectious cause of blindness and the most common sexually transmitted bacterium.

Verrucomicrobia Phylum of bacteria

Verrucomicrobia is a phylum of Gram-negative bacteria that contains only a few described species. The species identified have been isolated from fresh water, marine and soil environments and human faeces. A number of as-yet uncultivated species have been identified in association with eukaryotic hosts including extrusive explosive ectosymbionts of protists and endosymbionts of nematodes residing in their gametes.

<i>Chlamydia pneumoniae</i> Species of bacterium

Chlamydia pneumoniae is a species of Chlamydia, an obligate intracellular bacterium that infects humans and is a major cause of pneumonia. It was known as the Taiwan acute respiratory agent (TWAR) from the names of the two original isolates – Taiwan (TW-183) and an acute respiratory isolate designated AR-39. Briefly, it was known as Chlamydophila pneumoniae, and that name is used as an alternate in some sources. In some cases, to avoid confusion, both names are given.

<i>Chlamydia psittaci</i> Species of bacterium

Chlamydia psittaci is a lethal intracellular bacterial species that may cause endemic avian chlamydiosis, epizootic outbreaks in mammals, and respiratory psittacosis in humans. Potential hosts include feral birds and domesticated poultry, as well as cattle, pigs, sheep, and horses. C. psittaci is transmitted by inhalation, contact, or ingestion among birds and to mammals. Psittacosis in birds and in humans often starts with flu-like symptoms and becomes a life-threatening pneumonia. Many strains remain quiescent in birds until activated by stress. Birds are excellent, highly mobile vectors for the distribution of chlamydia infection, because they feed on, and have access to, the detritus of infected animals of all sorts.

Chlamydophila Genus of bacteria

Chlamydophila is a controversial bacterial genus belonging to the family Chlamydiaceae, order Chlamydiales, class/phylum Chlamydiae.

Chlamydiaceae Family of bacteria

The Chlamydiaceae are a family of gram-negative bacteria that belongs to the phylum Chlamydiae, order Chlamydiales. Chlamydiaceae species express the family-specific lipopolysaccharide epitope αKdo-(2→8)-αKdo-(2→4)-αKdo. Chlamydiaceae ribosomal RNA genes all have at least 90% DNA sequence identity. Chlamydiaceae species have varying inclusion morphology, varying extrachromosomal plasmid content, and varying sulfadiazine resistance.

Chlamydia muridarum is an intracellular bacterial species that at one time belonged to Chlamydia trachomatis. However, C. trachomatis naturally only infects humans and C. muridarum naturally infects only members of the family Muridae.

Chlamydia suis is a member of the genus Chlamydia. C. suis has only been isolated from swine, in which it may be endemic. Glycogen has been detected in Chlamydia suis inclusions in infected swine tissues and in cell culture. C. suis is associated with conjunctivitis, enteritis and pneumonia in swine.

Parachlamydiaceae is a family of bacteria in the order Chlamydiales. Species in this family have a Chlamydia–like cycle of replication and their ribosomal RNA genes are 80–90% identical to ribosomal genes in the Chlamydiaceae. The Parachlamydiaceae naturally infect amoebae and can be grown in cultured Vero cells. The Parachlamydiaceae are not recognized by monoclonal antibodies that detect Chlamydiaceae lipopolysaccharide.

Candidatus Rhabdochlamydia is a genus of intracellular bacteria; a separate family, Candidatus Rhabdochlamydiaceae, has been proposed for this genus. Candidatus Rhabdochlamydia species have not been cultured in vitro and have not been deposited in culture collections.

<i>Chlamydia abortus</i> Species of bacterium

Chlamydia abortus is a species in Chlamydiae that causes abortion and fetal death in mammals, including humans. Chlamydia abortus was renamed in 1999 as Chlamydophila psittaci along with all Chlamydiae except Chlamydia trachomatis. This was based on a lack of evident glycogen production and on resistance to the antibiotic sulfadiazine. In 1999 C. psittaci and C. abortus were recognized as distinct species based on differences of pathogenicity and DNA–DNA hybridization. In 2015, this new name was reverted to Chlamydia.

Chlamydia felis is a Gram-negative, obligate intracellular bacterial pathogen that infects cats. It is endemic among domestic cats worldwide, primarily causing inflammation of feline conjunctiva, rhinitis and respiratory problems. C. felis can be recovered from the stomach and reproductive tract. Zoonotic infection of humans with C. felis has been reported. Strains FP Pring and FP Cello have an extrachromosomal plasmid, whereas the FP Baker strain does not. FP Cello produces lethal disease in mice, whereas the FP Baker does not. An attenuated FP Baker strain, and an attenuated 905 strain, are used as live vaccines for cats.

Chlamydia caviae is a bacterium that can be recovered from the conjunctiva of Guinea pigs suffering from ocular inflammation and eye discharge. It is also possible to infect the genital tract of Guinea pigs with C. caviae and elicit a disease that is very similar to human Chlamydia trachomatis infection. C. caviae infects primarily the mucosal epithelium and is not invasive.

Chlamydia pecorum, also known as Chlamydophila pecorum is a species of Chlamydiaceae that originated from ruminants, such as cattle, sheep and goats. It has also infected koalas and swine. C. pecorum strains are serologically and pathogenically diverse.

<i>Chlamydia</i> (genus) Genus of bacteria

Chlamydia is a genus of pathogenic Gram-negative bacteria that are obligate intracellular parasites. Chlamydia infections are the most common bacterial sexually transmitted diseases in humans and are the leading cause of infectious blindness worldwide.

Chlamydia is a sexually transmitted infection caused by the bacterium Chlamydia trachomatis.

Parachlamydia acanthamoebae are bacterium that fall into the category of host-associated microorganisms. This bacterium lives within free-living amoebae that are an intricate part of their reproduction. Originally named Candidatus Parachlamydia acanthamoebae, its current scientific name was introduced shortly after. This species has shown to have over eighty percent 16S rRNA gene sequencing identity with the class Chlamydiae. Parachlamydia acanthamoebae has the same family as the genus Neochlamydia with which it shares many similarities.

Chlamydia research is the systematic study of the organisms in the taxonomic group of bacteria Chlamydiae, the diagnostic procedures to treat infections, the disease chlamydia, infections caused by the organisms, the epidemiology of infection and the development of vaccines. The process of research can include the participation of many researchers who work in collaboration from separate organizations, governmental entities and universities.

References

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  20. ↑ Stride MC, Polkinghorne A, Miller TL, Groff JM, Lapatra SE, Nowak BF (2013). "Molecular characterization of Parilichlamydia carangidicola, a novel Chlamydia-like epitheliocystis agent in yellowtail kingfish, Seriola lalandi (Valenciennes), and the proposal of a new family, Parilichlamydiaceae fam. nov. (order Chlamydiales)". Appl Environ Microbiol. 79 (5): 1590–1597. doi:10.1128/AEM.02899-12. PMC   3591964 . PMID   23275507.
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  26. 1 2 Horn M, Collingro A, Schmitz-Esser S, Beier C, Purkhold U, Fartmann B, Brandt P, Nyakatura G, Droege M, Frishman D, Rattei T, Mewes H, Wagner M (2004). "Illuminating the evolutionary history of chlamydiae". Science. 304 (5671): 728–30. Bibcode:2004Sci...304..728H. doi:10.1126/science.1096330. PMID   15073324. S2CID   39036549.
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  31. ↑ Griffiths E, Gupta RS (August 2007). "Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae". Microbiology. 153 (Pt 8): 2648–54. doi:10.1099/mic.0.2007/009118-0. PMID   17660429. S2CID   2094762.
  32. ↑ Corsaro D, Greub G (2006). "Pathogenic Potential of Novel Chlamydiae and Diagnostic Approaches to Infections Due to These Obligate Intracellular Bacteria". Clin Microbiol Rev. 19 (2): 283–97. doi:10.1128/CMR.19.2.283-297.2006. PMC   1471994 . PMID   16614250.
  33. ↑ All-Species Living Tree Project . Data extracted from the "16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database . Retrieved 2016-03-20.
  34. ↑ List of Prokaryotic names with Standing in Nomenclature. Data extracted from the "Chlamydiae". Archived from the original on 2011-06-13. Retrieved 2016-03-20.
  35. ↑ National Center for Biotechnology Information Data extracted from Sayers; et al. "Chlamydiae". National Center for Biotechnology Information . Retrieved 2016-03-20.
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