''Parachlamydia acanthamoebae'' are

bacterium Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the ...

that fall into the category of host-associated

microorganisms A microorganism, or microbe, is an organism of microscopic size, which may exist in its single-celled form or as a colony of cells. The possible existence of unseen microbial life was suspected from antiquity, with an early attestation in ...

. This

lives within free-living amoebae that are an intricate part of their

reproduction Reproduction (or procreation or breeding) is the biological process by which new individual organisms – "offspring" – are produced from their "parent" or parents. There are two forms of reproduction: Asexual reproduction, asexual and Sexual ...

. Originally named ''Candidatus Parachlamydia acanthamoebae'', its current

scientific name In Taxonomy (biology), taxonomy, binomial nomenclature ("two-term naming system"), also called binary nomenclature, is a formal system of naming species of living things by giving each a name composed of two parts, both of which use Latin gramm ...

was introduced shortly after. This

species A species () is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of Taxonomy (biology), ...

has shown to have over eighty percent

16S rRNA 16S ribosomal RNA (or 16Svedberg, S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome (SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as ...

gene sequencing identity with the class Chlamydiia. ''Parachlamydia acanthamoebae'' has the same family as the

genus Genus (; : genera ) is a taxonomic rank above species and below family (taxonomy), family as used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In bino ...

''Neochlamydia'' with which it shares many similarities.

Discovery

The isolation of ''Parachlamydia acanthamoebae'' is credited to Rolf Michel and Barbel Hauroder-Philippczyk in

Berlin Berlin ( ; ) is the Capital of Germany, capital and largest city of Germany, by both area and List of cities in Germany by population, population. With 3.7 million inhabitants, it has the List of cities in the European Union by population withi ...

in 1994. Using a nasal swab from volunteers, they were able to isolate coccoid-shaped

bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...

that were present among other naturally-produced

organisms An organism is any living thing that functions as an individual. Such a definition raises more problems than it solves, not least because the concept of an individual is also difficult. Many criteria, few of them widely accepted, have been pr ...

. Although at least ten subsequent attempts at reisolation were tried, ''P. acanthamoebae'' was not isolated again until 1997 when the researchers Rudolf Amann, Nina Springer, and Wolfgang Ludwig isolated it with a strain of '' Acanthamoeba'' species. This sample was transferred to a non-nutrient

agar Agar ( or ), or agar-agar, is a jelly-like substance consisting of polysaccharides obtained from the cell walls of some species of red algae, primarily from " ogonori" and " tengusa". As found in nature, agar is a mixture of two components, t ...

plate and the parasitized trophozoite of the '' Acanthamoeba'' species multiplied. A trophozoite is an active stage in the '' Acanthamoeba'' species life cycle in which the

protozoan Protozoa (: protozoan or protozoon; alternative plural: protozoans) are a polyphyletic group of single-celled eukaryotes, either free-living or parasitic, that feed on organic matter such as other microorganisms or organic debris. Historically ...

grows and feeds. The researchers were able to isolate the infected trophozoites by this method only once, as subsequent tries were unsuccessful. The researchers then took small aliquots of the

organism An organism is any life, living thing that functions as an individual. Such a definition raises more problems than it solves, not least because the concept of an individual is also difficult. Many criteria, few of them widely accepted, have be ...

and filtered it to ensure the sample was pure. After running these samples through a centrifuge, a machine with a rapid rotating inner container, the samples were used to directly amplify the

gene to form a nearly full-length

rRNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal ...

sequence by

Polymerase Chain Reaction The polymerase chain reaction (PCR) is a method widely used to make millions to billions of copies of a specific DNA sample rapidly, allowing scientists to amplify a very small sample of DNA (or a part of it) sufficiently to enable detailed st ...

. The ribosomal

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

was sequenced using the T7 sequencing kit of Pharmacia. After analyzing the

genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

and confirming 86% 16S rRNA gene sequence identity to members of the

''Chlamydia'', they proposed ''Parachlamydia acanthamoebae'' be classified under the order of Chlamydiales.

Phylogeny

Amann et al. used a number of methods to analyze the

phylogeny A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or Taxon, taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, M ...

of ''Parachlamydia acanthamoebae''. They were able to amplify

fragments that covered almost all of the

operon using PCR. A distance matrix was used to compare the attained 16S and 23S

sequences with the

with other

in the Chlamydia family as well as other

from known

phyla Phyla, the plural of ''phylum'', may refer to: * Phylum, a biological taxon between Kingdom and Class * by analogy, in linguistics, a large division of possibly related languages, or a major language family which is not subordinate to another Phy ...

. The ARB Project and the FastDNAml tool were used to perform maximum parsimony and maximum likelihood analyses. The maximum likelihood analysis was performed by comparing the

sequence from ''Parachlamydia acanthamoebae'' to

sequences from the entire ARB Project database. The maximum likelihood analysis compared the ''P. acanthamoebae''

sequences with the same

used in the distance matrix. Their analyses showed that ''P. acanthamoebae'' has an 86 to 87% sequence similarity with

in the Chlamydia

. It had a sequence similarity of 70 to 75% when compared to

from other

in the same domain. From this information, they proposed that the

are likely a novel member of a

in the family Chlamydiaceae. Everett et al. set out to determine the characteristics that specifically distinguish all the families in the order Chlamydiales, and in doing so proposed that the formation of the family Parachlamydiaceae. They used Sequencher data analysis tools to accumulate 23S

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

sequences from

in all of the families within Chlamydiales. Sequence information for the

genes In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

of these

was collected from

GenBank The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a par ...

. They used the Clustal W program to align all of the 16S and 23S data that was collected. PAUP version 4.0 was used to create maximum parsimony and neighbor-joining

phylogenetic In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...

trees. They found that ''P. acanthamoebae'' has a

sequence that is 15% different and a 23S

sequence that is 17% different from members of the family Chlamydiaceae. From this, they proposed the formation of a new family, Parachlamydiaceae, where ''P. acanthamoebae'' is currently classified under.

Genomic information

Greub et al. states that although there was a previous attempt to sequence the

of ''P. acanthamoebae'', the absence of a bridge element that helps with the assembly of the sequence and the repair of gaps made it difficult for researchers to completely sequence its

Pyrosequencing Pyrosequencing is a method of DNA sequencing (determining the order of nucleotides in DNA) based on the "sequencing by synthesis" principle, in which the sequencing is performed by detecting the nucleotide incorporated by a DNA polymerase. Pyrosequ ...

using the GS20 method and Solatex technology sequenced 1.6 Mbp of raw reads that each contained 36 bp, which were assembled into 95 contigs using GS20 reads. These reads were assembled in 8616 overlapping sequences that helped to further develop the

. Through

comparative genomics Comparative genomics is a branch of biological research that examines genome sequences across a spectrum of species, spanning from humans and mice to a diverse array of organisms from bacteria to chimpanzees. This large-scale holistic approach c ...

with the family '' Chlamydiaceae'' and the species ''Protochlamydia amoebophilia'', a GC content of 35-36% and an approximate

size of 2.4-3 Mbp were concluded. Further analysis of the genome of ''P. acanthamoebae'' shows that this

has

that encode a

chemotaxis Chemotaxis (from ''chemical substance, chemo-'' + ''taxis'') is the movement of an organism or entity in response to a chemical stimulus. Somatic cells, bacteria, and other single-cell organism, single-cell or multicellular organisms direct thei ...

system that is similar to the system found in

Escherichia coli ''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Escherichia'' that is commonly fo ...

. No other

in Chlamydiales have been found to encode for a system similar to the one present in ''P. acanthamoebae''. This

system encodes for at least 15

proteins Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, re ...

. Collingro et al. believe this system to be functional, as they found no

mutations In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mitosi ...

in the

sequences for these

. The specific role of this

system in ''P. acanthamoebae'' is unclear, however, since this

is non- motile.

Physiology

''Parachlamydia acanthamoebae'' is widely distributed in nature, being found in aquatic as well as terrestrial environments. Due to this organism's symbiotic relationship with Acanthamoeba, it has the ability to survive a wide array of environmental stresses. It is a coccoid

with a

diameter In geometry, a diameter of a circle is any straight line segment that passes through the centre of the circle and whose endpoints lie on the circle. It can also be defined as the longest Chord (geometry), chord of the circle. Both definitions a ...

of 0.5 um that has a variable reaction to gram staining. It is a

mesophilic A mesophile is an organism that grows best in moderate temperature, neither too hot nor too cold, with an optimum growth range from . The optimum growth temperature for these organisms is 37 °C (about 99 °F). The term is mainly applied ...

that can be grown on Vero cells.

Developmental stages

Similar to other Chlamydiales, it is commonly found in two developmental stages, the first of which is the elementary body, which is the infective stage of the

. The other developmental stage it is commonly found in is the reticulate body, which is its metabolically active dividing stage. However, ''Parachlamydia acanthamoebae'' and

within the family Parachlamydiaceae can also be found a crescent body stage, which has been found to be a more efficient infective stage for the

. The elementary body has been found to be the most dominant stage this

resides in once within an amoeba. Studies found that the elementary bodies were mainly found in vacuoles, and as incubation time continued, the

continued to replicate within the

vacuole A vacuole () is a membrane-bound organelle which is present in Plant cell, plant and Fungus, fungal Cell (biology), cells and some protist, animal, and bacterial cells. Vacuoles are essentially enclosed compartments which are filled with water ...

. Researchers were able to show that ''Parachlamydia acanthamoebae'' is mainly found in the reticulate body stage while it is present in the

cytoplasm The cytoplasm describes all the material within a eukaryotic or prokaryotic cell, enclosed by the cell membrane, including the organelles and excluding the nucleus in eukaryotic cells. The material inside the nucleus of a eukaryotic cell a ...

. This

was only in the crescent body stage after a significant incubation time, and even then it was only found within vacuoles and not in the

of the infected amoeba. The only stage that this

was proven to be in outside of the amoeba was the elementary stage.

Life cycle

The ''Parachlamydia acanthamoebae'' begins its life cycle by entering the amoeba by

phagocytosis Phagocytosis () is the process by which a cell (biology), cell uses its plasma membrane to engulf a large particle (≥ 0.5 μm), giving rise to an internal compartment called the phagosome. It is one type of endocytosis. A cell that performs ph ...

in either the elementary stage or the crescent stage. During this time, it begins to acquire the endosomal and lysosomal integral

glycoprotein Glycoproteins are proteins which contain oligosaccharide (sugar) chains covalently attached to amino acid side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known a ...

, designated Lamp-1. Once within the amoebic cell, the

changes its morphology to the reticulate body, where it then replicates by binary fission. Once in this stage, they can then leave the

, and enter the

. During the time that the amoeba is infected, it begins to increase significantly in size. This can be attributed to the increase in vacuoles in the

that contain ''Parachlamydia acanthamoebae''. Replication of the

continues until the amoeba lyses.

Pathogenicity

In Humans

''Parachlamydia acanthamoebae'' has been shown to infect and multiply in

simian The simians, anthropoids, or higher primates are an infraorder (Simiiformes ) of primates containing all animals traditionally called monkeys and apes. More precisely, they consist of the parvorders New World monkey, Platyrrhini (New World mon ...

and human cells. Experimental models were able to demonstrate that this

can enter, replicate, and lyse in human

macrophages Macrophages (; abbreviated MPhi, φ, MΦ or MP) are a type of white blood cell of the innate immune system that engulf and digest pathogens, such as cancer cells, microbes, cellular debris and foreign substances, which do not have proteins that ...

and pneumocytes. A study in 2003 examined ''P. acanthamoebae’s'' ability to enter and survive in human

. These researchers collected human

and placed these cells on growth plates in conjunction with ''P. acanthamoebae''. The results for this study showed that after an 8-hour time period, eighty percent of the

incubated with live ''P. acanthamoebae'' were infected with an average of 3.8

and were located in vacuoles. Their results also shows that the ''P. acanthamoebae'' cells continued to replicate within the

, and eventually caused

apoptosis Apoptosis (from ) is a form of programmed cell death that occurs in multicellular organisms and in some eukaryotic, single-celled microorganisms such as yeast. Biochemistry, Biochemical events lead to characteristic cell changes (Morphology (biol ...

. Although research on this

and how it can affect humans is minimal, there are several studies that link ''P. acanthamoebae'' to the onset of illnesses in humans. The diseases that have been connected to this

primarily affect the

respiratory system The respiratory system (also respiratory apparatus, ventilatory system) is a biological system consisting of specific organs and structures used for gas exchange in animals and plants. The anatomy and physiology that make this happen varies grea ...

. Research shows that

pneumonia Pneumonia is an Inflammation, inflammatory condition of the lung primarily affecting the small air sacs known as Pulmonary alveolus, alveoli. Symptoms typically include some combination of Cough#Classification, productive or dry cough, ches ...

bronchitis Bronchitis is inflammation of the bronchi (large and medium-sized airways) in the lungs that causes coughing. Bronchitis usually begins as an infection in the nose, ears, throat, or sinuses. The infection then makes its way down to the bronchi. ...

, and

atherosclerosis Atherosclerosis is a pattern of the disease arteriosclerosis, characterized by development of abnormalities called lesions in walls of arteries. This is a chronic inflammatory disease involving many different cell types and is driven by eleva ...

are among the most common complications that have arisen from ingestion of this

by humans. Although these studies show that ''P. acanthamoebae'' is linked to human diseases, researchers have not been able to isolate this

directly from a human.

Presence in Water Treatment Plants

In a study that assessed whether different

were present in a water treatment plant, ''P. acanthamoebae'' had been found in the river water that fed the water treatment plant that was used in the experiment. These researchers looked at the different steps within the water treatment facility, including sand filtration, followed by

ozonation Ozone () (or trioxygen) is an inorganic molecule with the chemical formula . It is a pale blue gas with a distinctively pungent smell. It is an allotrope of oxygen that is much less stable than the diatomic allotrope , breaking down in the low ...

, and finally granular

activated carbon Activated carbon, also called activated charcoal, is a form of carbon commonly used to filter contaminants from water and air, among many other uses. It is processed (activated) to have small, low-volume pores that greatly increase the surface ar ...

filtration, also known as GAC. They found this

within a

biofilm A biofilm is a Syntrophy, syntrophic Microbial consortium, community of microorganisms in which cell (biology), cells cell adhesion, stick to each other and often also to a surface. These adherent cells become embedded within a slimy ext ...

around the GAC. From this finding, the researchers concluded that this

was able to bypass the

step of the water treatment, which means it passed through this step inside an undetected '' Acanthamoeba'' species. This shows that it can protect itself from the harsh conditions in the treatment facility, or that the

itself is resistant to

In Cattle

''P. acanthamoebae'' has also been implicated as an abortive agent when it is present in

Swiss Swiss most commonly refers to: * the adjectival form of Switzerland * Swiss people Swiss may also refer to: Places * Swiss, Missouri * Swiss, North Carolina * Swiss, West Virginia * Swiss, Wisconsin Other uses * Swiss Café, an old café located ...

cattle. Researchers in

Switzerland Switzerland, officially the Swiss Confederation, is a landlocked country located in west-central Europe. It is bordered by Italy to the south, France to the west, Germany to the north, and Austria and Liechtenstein to the east. Switzerland ...

randomly selected 235 late term abortions in cattle during the breeding season of 2003 and 2004 and used PCR to detect the presence of this

in the sample. They found that 43 of the 235 cases tested positive for the presence of ''P. acanthamoebae''. Further examination of these positive cases showed that 25 of the 43 cases showed necrotizing placentitis and 35 of the 43 cases were confirmed positive by the presence of the

antibody An antibody (Ab) or immunoglobulin (Ig) is a large, Y-shaped protein belonging to the immunoglobulin superfamily which is used by the immune system to identify and neutralize antigens such as pathogenic bacteria, bacteria and viruses, includin ...

that was elicited against the bacterial infection. Not only is this detrimental to the cattle infected with the

, but it also poses a

zoonotic A zoonosis (; plural zoonoses) or zoonotic disease is an infectious disease of humans caused by a pathogen (an infectious agent, such as a virus, bacterium, parasite, fungi, or prion) that can jump from a non-human vertebrate to a human. When h ...

risk to humans because handling this aborted material could facilitate the contraction of

Antibiotic resistance and susceptibilities

''P. acanthamoebae'' has shown that it is affected by the presence of

antibiotics An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting pathogenic bacteria, bacterial infections, and antibiotic medications are widely used in the therapy ...

when it is inside of the host. One study analyzed two strains of ''P. acanthamoebae'', the Hall's Coccus strain and the BN9 strain, and tested their response to a number of common

. They cultured '' Acanthamoeba polyphaga'', a common

endosymbiotic An endosymbiont or endobiont is an organism that lives within the body or cells of another organism. Typically the two organisms are in a mutualistic relationship. Examples are nitrogen-fixing bacteria (called rhizobia), which live in the root ...

host of ''P. acanthamoebae'', in a PYG medium and added 20 μl of ''P. acanthamoebae'' to the growth plates. A portion of the amoeba were left both drug-free and free of ''P. acanthamoebae'' as a control to measure amoebal viability in the medium. Another portion was only subjected to

. The purpose of this is to serve as a control to assess if the amoeba itself displayed any

antibiotic An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting pathogenic bacteria, bacterial infections, and antibiotic medications are widely used in the therapy ...

toxicity. In this experiment, they found that ''Acanthamoeba polyphaga'' was not effected by any of the tested

. They found that most of the beta-lactam

vancomycin Vancomycin is a glycopeptide antibiotic medication used to treat certain bacterial infections. It is administered intravenously ( injection into a vein) to treat complicated skin infections, bloodstream infections, endocarditis, bone an ...

, and fluoroquinolones had no effect on the growth of ''P. acanthamoebae''. Because of this, it can be inferred that these two strains of ''P. acanthamoeba'' are resistant to these

. However, both of these strains showed inhibited growth when in the presence of

macrolides Macrolides are a class of mostly natural products with a large macrocycle, macrocyclic lactone ring to which one or more deoxy sugars, usually cladinose and desosamine, may be attached. Macrolides belong to the polyketide class of natural prod ...

doxycycline Doxycycline is a Broad-spectrum antibiotic, broad-spectrum antibiotic of the Tetracycline antibiotics, tetracycline class used in the treatment of infections caused by bacteria and certain parasites. It is used to treat pneumonia, bacterial p ...

aminoglycosides Aminoglycoside is a medicinal chemistry, medicinal and bacteriology, bacteriologic category of traditional Gram-negative antibacterial medications that inhibit protein synthesis and contain as a portion of the molecule an amino-modified glycoside ...

, and rifampin. These results show that ''P. acanthamoebae'' shows susceptibility and resistance to

that is very different from other closely related

microbes A microorganism, or microbe, is an organism of microscopic size, which may exist in its single-celled form or as a colony of cells. The possible existence of unseen microbial life was suspected from antiquity, with an early attestation in ...

, such as ''

Chlamydia trachomatis ''Chlamydia trachomatis'' () is a Gram-negative, Anaerobic organism, anaerobic bacterium responsible for Chlamydia infection, chlamydia and trachoma. ''C. trachomatis'' exists in two forms, an extracellular infectious elementary body (EB) and an ...

'' or '' Chlamydophila pneumoniae''.

References

{{Taxonbar, from=Q7133891 Chlamydiota Bacteria described in 1997