Chlamydiae

Chlamydiae
Chlamydia trachomatis
Scientific classification
Domain: Bacteria
Phylum: Chlamydiae
Garrity & Holt 2012
Class: Chlamydiia
Gupta et al. 2016
Orders and families
Synonyms
  • Chlamydaeota Oren et al. 2015

The Chlamydiae are bacterial phylum and class whose members are obligate intracellular pathogens.[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 are termed obligate intracellular pathogens. Most intracellular Chlamydiae are located in an inclusion body or vacuole. Outside of 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.

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.

Nomenclature

In 1966, Chlamydiae were recognized as bacteria and the genus Chlamydia was validated.[8] The order Chlamydiales was created by Storz and Page in 1971. The class Chlamydiia was recently validly published.[9][10][11] Between 1989 and 1999, new families, genera, and species were recognized. The phylum Chlamydiae was established in Bergey's Manual of Systematic Bacteriology.[12] By 2006, genetic data for over 350 chlamydial lineages had been reported,[13]

Taxonomy and molecular signatures

The Chlamydiae currently contain eight validly named genera, and 14 candidatus genera.[14] The phylum presently consist of two orders (Chlamydiales, [Parachlamydiales) and nine families within a single class (Chlamydiia).[9][10] Only four of these families are validly named (Chlamydiaceae, Parachlamydiaceae, Simkaniaceae, Waddliaceae)[15][16] while five are described as Candidatus families (Clavichlamydiaceae, Criblamydiaceae, Parilichlamydiaceae, Piscichlamydiaceae, and Rhabdochlamydiaceae).[17][18][19] The Chlamydiales order as recently described contains the families Chlamydiaceae', and the Candidatus Clanchiamydiaceae, while the new Parachlamydiales' order harbours the remaining seven families.[9] 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.[9][20] 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.[9][20] 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.[21][22] 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.[9][20] 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.[9][20][23][24] 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.[25][26] Reports have varied as to whether the Chlamydiae are related to the Planctomycetales or Spirochaetes.[27][28] 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.[24] 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.[29] Comparison of ribosomal RNA genes has provided a phylogeny of known strains within Chlamydiae.[13]

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.[30] 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.[31]

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








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

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[32] and the NCBI[33]

References

  1. ↑ Wyrick P (2000). "Intracellular survival by Chlamydia". Cell Microbiol. 2 (4): 275–82. doi:10.1046/j.1462-5822.2000.00059.x. PMID 11207584.
  2. ↑ Jacquier N, Viollier PH, Greub G (2015). "The role of peptidoglycan in chlamydial cell division: towards resolving the chlamydial anomaly". FEMS Microbiol Rev. 39 (2): 262–275. doi:10.1093/femsre/fuv001. PMID 25670734.
  3. ↑ Malhotra M, Sood S, Mukherjee A, Muralidhar S, Bala M (September 2013). "Genital Chlamydia trachomatis: an update". Indian J. Med. Res. 138 (3): 303–16. PMC 3818592Freely accessible. PMID 24135174.
  4. ↑ Gupta RS (2011). "Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes". Antonie Van Leeuwenhoek. 100 (2): 171–182. doi:10.1007/s10482-011-9616-8. PMID 21717204.
  5. ↑ Horn M (2008). "Chlamydiae as symbionts in eukaryotes". Annu Rev Microbiol. 62: 113–131. doi:10.1146/annurev.micro.62.081307.162818. PMID 18473699.
  6. ↑ Abdelrahman YM, Belland RJ (2005). "The chlamydial developmental cycle". FEMS Microbiol Rev. 29 (5): 949–959. doi:10.1016/j.femsre.2005.03.002. PMID 16043254.
  7. ↑ Horn M, Collingro A, Schmitz-Esser S, Beier CL, Purkhold U, Fartmann B, Brandt P, Nyakatura GJ, Droege M, Frishman D, Rattei T, Mewes HW, Wagner M (2004). "Illuminating the evolutionary history of chlamydiae". Science. 304 (5671): 728–730. doi:10.1126/science.1096330. PMID 15073324.
  8. ↑ Moulder J (1966). "The relation of the psittacosis group (Chlamydiae) to bacteria and viruses". Annu Rev Microbiol. 20: 107–30. doi:10.1146/annurev.mi.20.100166.000543. PMID 5330228.
  9. 1 2 3 4 5 6 7 Gupta RS, Naushad S, Chokshi C, Griffiths E, Adeolu M (2015). "A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia". Antonie Van Leeuwenhoek. 108 (3): 765–781. doi:10.1007/s10482-015-0532-1. PMID 26179278.
  10. 1 2 Oren A, Garrity GM (2016). "List of new names and new combinations previously effectively, but not validly, published". Int J Syst Evol Microbiol. 66 (7): 2463–6. doi:10.1099/ijsem.0.001149. PMID 27530111.
  11. ↑ Storz J, Page LA (1971). "Taxonomy of the Chlamydiae: reasons for classifying organisms of the genus Chlamydia, family Chlamydiaceae, in a separate order, Chlamydiales ord. nov". International Journal of Systematic Bacteriology. 21 (4): 332–334. doi:10.1099/00207713-21-4-332.
  12. ↑ Garrity GM, Boone DR (editors) (2001). Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the Deeply Branching and Phototrophic Bacteria (2nd ed.). Springer. ISBN 0-387-98771-1.
  13. 1 2 Everett K, Thao M, Horn M, Dyszynski G, Baumann P (2005). "Novel chlamydiae in whiteflies and scale insects: endosymbionts 'Candidatus Fritschea bemisiae' strain Falk and 'Candidatus Fritschea eriococci' strain Elm". Int J Syst Evol Microbiol. 55 (Pt 4): 1581–7. doi:10.1099/ijs.0.63454-0. PMID 16014485.
  14. ↑ Sayers; et al. "Chlamydiia". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-10-24.
  15. ↑ Everett KD, Bush RM, Andersen AA (1999). "Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms". Int J Syst Bacteriol. 49 (Pt 2): 415–440. doi:10.1099/00207713-49-2-415. PMID 10319462.
  16. ↑ Rurangirwa FR, Dilbeck PM, Crawford TB, McGuire TC, McElwain TF (1999). "Analysis of the 16S rRNA gene of micro-organism WSU 86-1044 from an aborted bovine foetus reveals that it is a member of the order Chlamydiales: proposal of Waddliaceae fam. nov., Waddlia chondrophila gen. nov., sp. nov.". Int J Syst Bacteriol. 49 (Pt 2): 577–581. doi:10.1099/00207713-49-2-577. PMID 10319478.
  17. ↑ Thomas V, Casson N, Greub G (2006). "Criblamydia sequanensis, a new intracellular Chlamydiales isolated from Seine river water using amoebal co-culture". Environ Microbiol. 8 (12): 2125–2135. doi:10.1111/j.1462-2920.2006.01094.x. PMID 17107554.
  18. ↑ Stride MC, Polkinghorne A, Miller TL, Groff JM, Lapatra SE, Nowak BF (2013). "Molecular characterization of "Candidatus Parilichlamydia carangidicola," a novel Chlamydia-like epitheliocystis agent in yellowtail kingfish, Seriola lalandi (Valenciennes), and the proposal of a new family, "Candidatus Parilichlamydiaceae" fam. nov. (order Chlamydiales)". Appl Environ Microbiol. 79 (5): 1590–1597. doi:10.1128/AEM.02899-12. PMID 23275507.
  19. ↑ Kuo C-C, Horn M, Stephens RS (2011) Order I. Chlamydiales. In: Bergey’s Manual of Systematic Bacteriology, vol. 4, 2nd edn. pp. 844-845. Eds Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W. Springer-: New York.
  20. 1 2 3 4 Griffiths E, Ventresca MS, Gupta RS (2006). "BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species". BMC Genomics. 25 (7): 14. doi:10.1186/1471-2164-7-14. PMID 16436211.
  21. ↑ Sachse K, Bavoil PM, Kaltenboeck B, Stephens RS, Kuo CC, Rossello-Mora R, Horn M (2015). "Emendation of the family Chlamydiaceae: proposal of a single genus, Chlamydia, to include all currently recognized species". Appl Microbiol. 38 (2): 99–103.
  22. ↑ Oren A, Garrity GM (2015). "List of new names and new combinations previously effectively, but not validly, published". Int J Syst Evol Microbiol. 65: 2017–2025. doi:10.1099/ijs.0.000317.
  23. ↑ Greub G, Raoult D (2003). "History of the ADP/ATP-Translocase-Encoding Gene, a Parasitism Gene Transferred from a Chlamydiales Ancestor to Plants 1 Billion Years Ago". Appl Environ Microbiol. 69 (9): 5530–5. doi:10.1128/AEM.69.9.5530-5535.2003. PMC 194985Freely accessible. PMID 12957942.
  24. 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. doi:10.1126/science.1096330. PMID 15073324.
  25. ↑ Griffiths E, Petrich AK, Gupta RS (August 2005). "Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification". Microbiology (Reading, Engl.). 151 (Pt 8): 2647–57. doi:10.1099/mic.0.28057-0. PMID 16079343.
  26. ↑ Gupta RS, Griffiths E (December 2006). "Chlamydiae-specific proteins and indels: novel tools for studies". Trends Microbiol. 14 (12): 527–35. doi:10.1016/j.tim.2006.10.002. PMID 17049238.
  27. ↑ Ward N, Rainey F, Hedlund B, Staley J, Ludwig W, Stackebrandt E (2000). "Comparative phylogenetic analyses of members of the order Planctomycetales and the division Verrucomicrobia: 23S rRNA gene sequence analysis supports the 16S rRNA gene sequence-derived phylogeny". Int J Syst Evol Microbiol. 50 (6): 1965–72. doi:10.1099/00207713-50-6-1965. PMID 11155969.
  28. ↑ Teeling H, Lombardot T, Bauer M, Ludwig W, Glöckner F (2004). "Evaluation of the phylogenetic position of the planctomycete 'Rhodopirellula baltica' SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees". Int J Syst Evol Microbiol. 54 (Pt 3): 791–801. doi:10.1099/ijs.0.02913-0. PMID 15143026.
  29. ↑ 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 (Reading, Engl.). 153 (Pt 8): 2648–54. doi:10.1099/mic.0.2007/009118-0. PMID 17660429.
  30. ↑ 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 1471994Freely accessible. PMID 16614250.
  31. ↑ 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.
  32. ↑ List of Prokaryotic names with Standing in Nomenclature. Data extracted from the "Chlamydiae". Retrieved 2016-03-20.
  33. ↑ National Center for Biotechnology Information Data extracted from Sayers; et al. "Chlamydiae". National Center for Biotechnology Information. Retrieved 2016-03-20.

External links

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