Multilocus Sequence Typing
Tandem Repeat Sequences
Bacterial Typing Techniques
PCR amplification from fixed tissue indicates frequent involvement of Brachyspira aalborgi in human intestinal spirochetosis. (1/26)PCR procedures amplifying portions of the 16S rRNA and NADH oxidase genes of Brachyspira aalborgi and Serpulina pilosicoli were applied to DNA extracted from paraffin-embedded human colonic or rectal tissues from 30 Norwegian, Australian, and U.S. patients, 16 of whom had histologic evidence of intestinal spirochetosis (IS). B. aalborgi-specific sequences were identified by PCR in 10 of the IS patients (62.5%) but none of the others, while S. pilosicoli sequences were not detected in tissues from any patient. Direct sequencing of products from three of the positive samples provided further confirmation of the presence of B. aalborgi. B. aalborgi may be a more common cause of intestinal spirochetosis than has been previously thought. (+info)
Phenotypic and genotypic heterogeneity among cultivable pathogen-related oral spirochetes and Treponema vincentii. (2/26)Recent findings challenge the assumption that pathogen-related oral spirochetes (PROS) are related to Treponema pallidum. Treponema vincentii, grown in OMIZ-Pat media, cross-reacted with monoclonal antibody H9-2 against T. pallidum, and cultivable PROS had 16S rRNA gene sequences similar to those of T. vincentii (C.-B. Choi, C. Wyss, and U. B. Gobel. J. Clin. Microbiol. 34:1922-1925, 1996). Aims of the present study were to determine whether antigen phenotypes of oral treponemas were influenced by growth conditions and to evaluate the genetic relatedness of cultivable PROS to T. pallidum and T. vincentii. Results show that three T. pallidum monoclonal antibodies (H9-1, H9-2, and F5) cross-reacted with whole cells from four Treponema species grown in modified OMIZ-Pat medium, but not with treponemas grown in NOS medium. Only H9-2 reacted in immunoblots with reduced proteins from cultivable PROS and T. vincentii. Three of five PROS isolates were amplified by T. vincentii-specific PCR, and one was amplified by Treponema medium-specific PCR. None were amplified by T. pallidum-specific PCR. Three of five PROS isolates had 16S ribosomal DNA restriction fragment length polymorphism patterns identical to that of T. vincentii, and the patterns of two isolates resembled that of T. medium. Arbitrarily primed-PCR profiles from whole genomic DNA were distinct among five PROS isolates and two T. vincentii strains. Thus, PROS isolates represent a heterogeneous group of treponemas that share some 16S rRNA gene sequences with T. vincentii and T. medium, but not with T. pallidum. It is proposed that the PROS nomenclature be dropped. (+info)
Brachyspira aalborgi infection diagnosed by culture and 16S ribosomal DNA sequencing using human colonic biopsy specimens. (3/26)In this study we report on the isolation and characterization of the intestinal spirochete Brachyspira aalborgi using human mucosal biopsy specimens taken from the colon of a young adult male with intestinal spirochetosis. A selective medium, containing 400 microg of spectinomycin/ml and 5 microg of polymyxin/ml was used for the isolation procedure. A high degree of similarity, in terms of phenotypic properties and 16S ribosomal DNA sequence, was observed between the isolated strain, named W1, and the type strain, 513A, of B. aalborgi. A similarity of 99.7% in the nucleotide sequence was found between W1 and 513A(T), based on the almost-complete gene. A short segment of the 16S rRNA gene was amplified by PCR using genetic material enriched from paraffin-embedded biopsy specimens, which were taken from the patient on two occasions. The products showed 16S rRNA gene sequences virtually identical to that of strain 513A(T) in the actual region. Immunohistochemistry was performed on the colonic biopsy specimens with a polyclonal antibody raised against an intestinal spirochete isolated in a previous case of human intestinal spirochetosis. The antibody reacted strongly with the spirochete on the luminal epithelium. No immune reaction was seen within or below the surface epithelium. Routine histology did not reveal signs of colitis. Electron microscopy showed spirochetes attached end-on to the colonic mucosal surface. The isolate grew poorly on a commonly used selective medium for intestinal spirochetes, which may explain previous failures to isolate B. aalborgi. (+info)
Evaluation of blood culture systems for detection of the intestinal spirochaete Brachyspira (Serpulina) pilosicoli in human blood. (4/26)The anaerobic intestinal spirochaete Brachyspira (Serpulina) pilosicoli has been isolated from the bloodstream of French patients by manual blood culture systems. The purpose of this study was to determine whether the automated and manual blood culture systems used in Australia are suitable for growth and detection of this organism. Strains of B. pilosicoli were added to human blood to give concentrations ranging from 1 x 10(4) to 1 x 10(1) spirochaetes/ml and 10-ml volumes were inoculated into the media. Three strains of B. pilosicoli grew slowly in all manual Hemoline and BBL Septi-Chek formulations tested. Subcultures taken between 2 and 10 days after inoculation yielded growth only after incubation for a further 5-8 days. Growth and automated detection were achieved in the BACTEC system with Anaerobic/F medium with or without Fastidious Organism Supplement. Minimum time to signal for nine strains varied between 5.6 and 14.9 days, with a minimum concentration of 10(1) spirochaetes/ml of blood being detected. None of nine strains gave a positive signal in the BacT/Alert system when FAN Anaerobic culture bottles were used; however, four strains were detected by subculture taken at 7 or 14 days after inoculation. When Anaerobic medium was used in the BacT/Alert system, two of three strains gave a signal and the other strain grew and was detected by subculture. Spirochaetaemias caused by B. pilosicoli may be unrecognised because detection time by the signal or subculture exceeds 5 days. (+info)
Nitrogen fixation by symbiotic and free-living spirochetes. (5/26)Spirochetes from termite hindguts and freshwater sediments possessed homologs of a nitrogenase gene (nifH) and exhibited nitrogenase activity, a previously unrecognized metabolic capability in spirochetes. Fixation of 15-dinitrogen was demonstrated with termite gut Treponema ZAS-9 and free-living Spirochaeta aurantia. Homologs of nifH were also present in human oral and bovine ruminal treponemes. Results implicate spirochetes in the nitrogen nutrition of termites, whose food is typically low in nitrogen, and in global nitrogen cycling. These results also proffer spirochetes as a likely origin of certain nifHs observed in termite guts and other environments that were not previously attributable to known microbes. (+info)
Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes. (6/26)BACKGROUND: Analysis of any newly sequenced bacterial genome starts with the identification of protein-coding genes. Despite the accumulation of multiple complete genome sequences, which provide useful comparisons with close relatives among other organisms during the annotation process, accurate gene prediction remains quite difficult. A major reason for this situation is that genes are tightly packed in prokaryotes, resulting in frequent overlap. Thus, detection of translation initiation sites and/or selection of the correct coding regions remain difficult unless appropriate biological knowledge (about the structure of a gene) is imbedded in the approach. RESULTS: We have developed a new program that automatically identifies biologically significant candidate genes in a bacterial genome. Twenty-six complete prokaryotic genomes were analyzed using this tool, and the accuracy of gene finding was assessed by comparison with existing annotations. This analysis revealed that, despite the enormous effort of genome program annotators, a small but not negligible number of genes annotated within the framework of sequencing projects are likely to be partially inaccurate or plainly wrong. Moreover, the analysis of several putative new genes shows that, as expected, many short genes have escaped annotation. In most cases, these new genes revealed frameshifts that could be either artifacts or genuine frameshifts. Some entirely unexpected new genes have also been identified. This allowed us to get a more complete picture of prokaryotic genomes. The results of this procedure are progressively integrated into the SWISS-PROT reference databank. CONCLUSIONS: The results described in the present study show that our procedure is very satisfactory in terms of gene finding accuracy. Except in few cases, discrepancies between our results and annotations provided by individual authors can be accounted for by the nature of each annotation process or by specific characteristics of some genomes. This stresses that close cooperation between scientists, regular update and curation of the findings in databases are clearly required to reduce the level of errors in genome annotation (and hence in reducing the unfortunate spreading of errors through centralized data libraries). (+info)
Phylogenetic position and in situ identification of ectosymbiotic spirochetes on protists in the termite gut. (7/26)Phylogenetic relationships, diversity, and in situ identification of spirochetes in the gut of the termite Neotermes koshunensis were examined without cultivation, with an emphasis on ectosymbionts attached to flagellated protists. Spirochetes in the gut microbial community investigated so far are related to the genus Treponema and divided into two phylogenetic clusters. In situ hybridizations with a 16S rRNA-targeting consensus oligonucleotide probe for one cluster (known as termite Treponema cluster I) detected both the ectosymbiotic spirochetes on gut protists and the free-swimming spirochetes in the gut fluid of N. koshunensis. The probe for the other cluster (cluster II), which has been identified as ectosymbionts on gut protists of two other termite species, Reticulitermes speratus and Hodotermopsis sjoestedti, failed to detect any spirochete population. The absence of cluster II spirochetes in N. koshunensis was confirmed by intensive 16S ribosomal DNA (rDNA) clone analysis, in which remarkably diverse spirochetes of 45 phylotypes were identified, almost all belonging to cluster I. Ectosymbiotic spirochetes of the three gut protist species Devescovina sp., Stephanonympha sp., and Oxymonas sp. in N. koshunensis were identified by their 16S rDNA and by in situ hybridizations using specific probes. The probes specific for these ectosymbionts did not receive a signal from the free-swimming spirochetes. The ectosymbionts were dispersed in cluster I of the phylogeny, and they formed distinct phylogenetic lineages, suggesting multiple origins of the spirochete attachment. Each single protist cell harbored multiple spirochete species, and some of the spirochetes were common among protist species. The results indicate complex relationships of the ectosymbiotic spirochetes with the gut protists. (+info)
Analysis of genes of tetrahydrofolate-dependent metabolism from cultivated spirochaetes and the gut community of the termite Zootermopsis angusticollis. (8/26)The hindguts of wood-feeding termites are the sites of intense, CO2-reductive acetogenesis. This activity profoundly influences host nutrition and methane emissions. Homoacetogens previously isolated from diverse termites comprised novel taxa belonging to two distinct bacterial phyla, Firmicutes and Spirochates. Little else is known about either the diversity or abundance of homoacetogenic species present in any given termite or the genetic details underlying CO2-reductive acetogenesis by Spirochaetes. A key enzyme of CO2-reductive acetogenesis is formyltetrahydrofolate synthetase (FTHFS). A previously designed primer set was used to amplify FTHFS genes from three isolated termite-gut spirochaetes. Sequencing DNA flanking the FTHFS gene of Treponema strain ZAS-2 revealed genes encoding two acetogenesis-related enzymes, methenyltetrahydrofolate cyclohydrolase and methylenetetrahydrofolate dehydrogenase. Although termite-gut spirochaetes are only distantly related to clostridia at the ribosomal level, their tetrahydrofolate-dependent enzymes appear to be closely related. In contrast, homologous proteins identified in the non-homoacetogenic oral spirochaete Treponema denticola were only distantly related to those from clostridia and the termite-gut treponemes. Having demonstrated their utility with spirochaete pure cultures, the FTHFS primers were used to construct a 91-clone library from the termite-gut community DNA. From this, 19 DNA and eight amino acid FTHFS types were identified. Over 75 % of the retrieved clones formed a novel, coherent cluster with the FTHFS homologues obtained from the termite-gut treponemes. Thus, FTHFS gene diversity in the gut of the termite Zootermopsis angusticollis appears to be dominated by spirochaetes. The homoacetogenic capacity of termite-gut spirochaetes may have been acquired via lateral gene transfer from clostridia. (+info)
Spirochaetaceae is a family of spiral-shaped, gram-negative bacteria known as spirochetes. These bacteria are characterized by their unique morphology, which includes a flexible helical shape and the presence of endoflagella, which are located inside the cell wall and run lengthwise along the entire length of the organism. This arrangement of flagella allows the spirochete to move in a corkscrew-like motion.
Spirochaetaceae includes several genera of medically important bacteria, such as:
* Treponema: This genus includes the bacterium that causes syphilis (Treponema pallidum) and other treponemal diseases like yaws and pinta.
* Borrelia: This genus includes the spirochetes responsible for Lyme disease (Borrelia burgdorferi) and relapsing fever (Borrelia recurrentis).
* Leptospira: This genus contains the bacteria that cause leptospirosis, a zoonotic disease transmitted through the urine of infected animals.
Spirochetes are often found in aquatic environments and can be part of the normal microbiota of some animals, including humans. However, certain species can cause significant diseases in humans and animals, making them important pathogens. Proper identification and appropriate antibiotic treatment are crucial for managing spirochetal infections.
Minisatellites, also known as VNTRs (Variable Number Tandem Repeats), are repetitive DNA sequences that consist of a core repeat unit of 10-60 base pairs, arranged in a head-to-tail fashion. They are often found in non-coding regions of the genome and can vary in the number of times the repeat unit is present in an individual's DNA. This variation in repeat number can occur both within and between individuals, making minisatellites useful as genetic markers for identification and forensic applications. They are also associated with certain genetic disorders and play a role in genome instability.
Multilocus Sequence Typing (MLST) is a standardized method used in microbiology to characterize and identify bacterial isolates at the subspecies level. It is based on the sequencing of several (usually 7-10) housekeeping genes, which are essential for the survival of the organism and have a low rate of mutation. The sequence type (ST) is determined by the specific alleles present at each locus, creating a unique profile that can be used to compare and cluster isolates into clonal complexes or sequence types. This method provides high-resolution discrimination between closely related strains and has been widely adopted for molecular epidemiology, infection control, and population genetics studies of bacterial pathogens.
Tandem Repeat Sequences (TRS) in genetics refer to repeating DNA sequences that are arranged directly after each other, hence the term "tandem." These sequences consist of a core repeat unit that is typically 2-6 base pairs long and is repeated multiple times in a head-to-tail fashion. The number of repetitions can vary between individuals and even between different cells within an individual, leading to genetic heterogeneity.
TRS can be classified into several types based on the number of repeat units and their stability. Short Tandem Repeats (STRs), also known as microsatellites, have fewer than 10 repeats, while Minisatellites have 10-60 repeats. Variations in the number of these repeats can lead to genetic instability and are associated with various genetic disorders and diseases, including neurological disorders, cancer, and forensic identification.
It's worth noting that TRS can also occur in protein-coding regions of genes, leading to the production of repetitive amino acid sequences. These can affect protein structure and function, contributing to disease phenotypes.
Leptospira is a genus of spirochete bacteria that are thin and tightly coiled, with hooked ends. These bacteria are aerobic and can survive in a wide range of environments, but they thrive in warm, moist conditions. They are known to cause a disease called leptospirosis, which is transmitted to humans and animals through direct contact with the urine of infected animals or through contaminated water, soil, or food.
Leptospira bacteria can infect a wide range of hosts, including mammals, birds, reptiles, and amphibians. In animals, leptospirosis can cause a variety of symptoms, such as fever, muscle pain, kidney damage, and liver failure. In humans, the disease can also cause a range of symptoms, from mild flu-like illness to severe kidney and liver damage, meningitis, and respiratory distress.
There are several species of Leptospira, some of which are pathogenic (cause disease) and others that are non-pathogenic (do not cause disease). The pathogenic species include L. interrogans, L. kirschneri, L. borgpetersenii, L. santarosai, L. weilii, and L. alexanderi. These species contain more than 250 serovars (strains) that can cause leptospirosis in humans and animals.
Prevention of leptospirosis includes avoiding contact with contaminated water or soil, wearing protective clothing and footwear when working outdoors, vaccinating domestic animals against Leptospira infection, and controlling rodent populations. Treatment typically involves antibiotics such as doxycycline or penicillin, and supportive care for severe cases.
'Leptospira interrogans' is a bacterial species that belongs to the genus Leptospira. It is a spirochete, meaning it has a spiral or corkscrew-shaped body, and is gram-negative, which refers to its staining characteristics under a microscope. This bacterium is the primary pathogen responsible for leptospirosis, a zoonotic disease that affects both humans and animals. It is often found in the renal tubules of infected animals and can be shed through their urine, contaminating water and soil. Humans can become infected through direct contact with infected animal tissues or urine, or indirectly through exposure to contaminated environments. The clinical manifestations of leptospirosis range from mild flu-like symptoms to severe illness, including kidney failure, meningitis, and respiratory distress.
Bacterial typing techniques are methods used to identify and differentiate bacterial strains or isolates based on their unique characteristics. These techniques are essential in epidemiological studies, infection control, and research to understand the transmission dynamics, virulence, and antibiotic resistance patterns of bacterial pathogens.
There are various bacterial typing techniques available, including:
1. **Bacteriophage Typing:** This method involves using bacteriophages (viruses that infect bacteria) to identify specific bacterial strains based on their susceptibility or resistance to particular phages.
2. **Serotyping:** It is a technique that differentiates bacterial strains based on the antigenic properties of their cell surface components, such as capsules, flagella, and somatic (O) and flagellar (H) antigens.
3. **Biochemical Testing:** This method uses biochemical reactions to identify specific metabolic pathways or enzymes present in bacterial strains, which can be used for differentiation. Commonly used tests include the catalase test, oxidase test, and various sugar fermentation tests.
4. **Molecular Typing Techniques:** These methods use genetic markers to identify and differentiate bacterial strains at the DNA level. Examples of molecular typing techniques include:
* **Pulsed-Field Gel Electrophoresis (PFGE):** This method uses restriction enzymes to digest bacterial DNA, followed by electrophoresis in an agarose gel under pulsed electrical fields. The resulting banding patterns are analyzed and compared to identify related strains.
* **Multilocus Sequence Typing (MLST):** It involves sequencing specific housekeeping genes to generate unique sequence types that can be used for strain identification and phylogenetic analysis.
* **Whole Genome Sequencing (WGS):** This method sequences the entire genome of a bacterial strain, providing the most detailed information on genetic variation and relatedness between strains. WGS data can be analyzed using various bioinformatics tools to identify single nucleotide polymorphisms (SNPs), gene deletions or insertions, and other genetic changes that can be used for strain differentiation.
These molecular typing techniques provide higher resolution than traditional methods, allowing for more accurate identification and comparison of bacterial strains. They are particularly useful in epidemiological investigations to track the spread of pathogens and identify outbreaks.
Bacterial DNA refers to the genetic material found in bacteria. It is composed of a double-stranded helix containing four nucleotide bases - adenine (A), thymine (T), guanine (G), and cytosine (C) - that are linked together by phosphodiester bonds. The sequence of these bases in the DNA molecule carries the genetic information necessary for the growth, development, and reproduction of bacteria.
Bacterial DNA is circular in most bacterial species, although some have linear chromosomes. In addition to the main chromosome, many bacteria also contain small circular pieces of DNA called plasmids that can carry additional genes and provide resistance to antibiotics or other environmental stressors.
Unlike eukaryotic cells, which have their DNA enclosed within a nucleus, bacterial DNA is present in the cytoplasm of the cell, where it is in direct contact with the cell's metabolic machinery. This allows for rapid gene expression and regulation in response to changing environmental conditions.
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- Syphilis is an infectious disease caused by Treponema pallidum, which belongs to the Spirochaetaceae family. (medscape.com)
- Treponema pallidum is an aerobic, Gram-negative bacterium in the Spirochaetaceae family which is spiral in shape. (hartmann-academie.nl)
- While Methanomassiliicoccacaea were enriched in ZF/C76 supplemented biodigester due to a significant increase in hydrogen partial pressure, probably caused by the enrichment of Spirochaetaceae (genus Treponema). (aucegypt.edu)
- Leptospira spp belonging to family spirochaetaceae. (noplag.com)
- Homoe reminded Spirochaetaceae, pursuits, buy cheap effexor purchase tablets and nevertheless scrubbers qua a ammiaceous separableness. (pipelink.com.sg)
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- 17. Which of the following genus belongs to family Spirochaetaceae? (grabstudy.com)