56-530: H. aegyptius H. ducreyi H. felis H. haemoglobinophilus H. haemolyticus H. influenzae H. parainfluenzae H. paracuniculus H. parahaemolyticus H. paraphrohaemolyticus H. pittmaniae H. piscium H. sputorum Haemophilus is a genus of Gram-negative , pleomorphic , coccobacilli bacteria belonging to the family Pasteurellaceae . While Haemophilus bacteria are typically small coccobacilli, they are categorized as pleomorphic bacteria because of
112-728: A bacterial genome over three types of outbreak contact networks—homogeneous, super-spreading, and chain-like. They summarized the resulting phylogenies with five metrics describing tree shape. Figures 2 and 3 illustrate the distributions of these metrics across the three types of outbreaks, revealing clear differences in tree topology depending on the underlying host contact network. Super-spreader networks give rise to phylogenies with higher Colless imbalance, longer ladder patterns, lower Δw, and deeper trees than those from homogeneous contact networks. Trees from chain-like networks are less variable, deeper, more imbalanced, and narrower than those from other networks. Scatter plots can be used to visualize
168-568: A biogroup of H. influenzae . In 1984, 10 children in the town of Promissão in Sao Paulo, Brazil, developed a sudden and severe illness after a recent bout (within the last 30 days) of conjunctivitis – Brazilian Purpuric Fever (BPF). Scientists were able to isolate H. influenzae biogroup aegyptius after studying the blood and cerebrospinal fluids of affected children. After discovering another, and very similar, outbreak in Londrina (located
224-499: A disproof of a previously widely accepted theory. During the late 19th century, Ernst Haeckel 's recapitulation theory , or "biogenetic fundamental law", was widely popular. It was often expressed as " ontogeny recapitulates phylogeny", i.e. the development of a single organism during its lifetime, from germ to adult, successively mirrors the adult stages of successive ancestors of the species to which it belongs. But this theory has long been rejected. Instead, ontogeny evolves –
280-637: A highly virulent clonal group of Haemophilus aegyptius , localized in and around the São Paulo state of Brazil , was found to be responsible for Brazilian purpuric fever , an acute septicemic fulminant illness affecting children. Haemophilus aegyptius was first observed by Koch in 1883. Under the German Cholera Commission of Egypt, Koch studied 50 patients in Egypt who were suffering from Egyptian eye disease. He discovered this disease
336-536: A language as an evolutionary system. The evolution of human language closely corresponds with human's biological evolution which allows phylogenetic methods to be applied. The concept of a "tree" serves as an efficient way to represent relationships between languages and language splits. It also serves as a way of testing hypotheses about the connections and ages of language families. For example, relationships among languages can be shown by using cognates as characters. The phylogenetic tree of Indo-European languages shows
392-692: A little under 200 miles from Promissao), scientists determined that a single H. influenzae biogroup aegyptius clone is responsible for all cases of BPF. In his classic paper, Weeks characterizes H. aegyptius by its high contagiousness, direct transmission from patient to volunteer, pathogenesis , pathology , treatment and epidemiology. It manifests itself most often as BPF in infants and young children, aged 3 months to 8 years. Symptoms of Brazilian Purpuric Fever are usually preceded by purulent conjunctivitis and later include acute, or sudden, onset of high fever, vomiting, abdominal pain, purpura, vascular collapse and death. The overall patient fatality rate since
448-402: A lot of effort to classify this bacteria. So far, no one test standing alone has been able to differentiate these two bacteria; however, through compound efforts of different scientists and different tests scientists have gained a greater understanding of the relationship between these two bacteria. In order to account for both the similarities and differences, H. aegyptius has been classified as
504-417: A phylogenetic tree can be living taxa or fossils , which represent the present time or "end" of an evolutionary lineage, respectively. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor of the tree. An unrooted tree diagram (a network) makes no assumption about the ancestral line, and does not show the origin or "root" of the taxa in question or
560-451: A separate species. Others, like Brenner et al. stand by a historical viewpoint that the two species are one and the same, with H. influenzae being the older name, and thus the name with higher priority. These bacteria are curious in that they are phylogenetically one species but differ phenotypically ; they share the same historical pattern but have clinical differences. Today, the issue remains unresolved, although scientists have put in
616-700: A shared evolutionary history. There are debates if increasing the number of taxa sampled improves phylogenetic accuracy more than increasing the number of genes sampled per taxon. Differences in each method's sampling impact the number of nucleotide sites utilized in a sequence alignment, which may contribute to disagreements. For example, phylogenetic trees constructed utilizing a more significant number of total nucleotides are generally more accurate, as supported by phylogenetic trees' bootstrapping replicability from random sampling. The graphic presented in Taxon Sampling, Bioinformatics, and Phylogenomics , compares
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#1732772775585672-462: A significant source of error within phylogenetic analysis occurs due to inadequate taxon samples. Accuracy may be improved by increasing the number of genetic samples within its monophyletic group. Conversely, increasing sampling from outgroups extraneous to the target stratified population may decrease accuracy. Long branch attraction is an attributed theory for this occurrence, where nonrelated branches are incorrectly classified together, insinuating
728-631: A single tree with true claim. The same process can be applied to texts and manuscripts. In Paleography , the study of historical writings and manuscripts, texts were replicated by scribes who copied from their source and alterations - i.e., 'mutations' - occurred when the scribe did not precisely copy the source. Phylogenetics has been applied to archaeological artefacts such as the early hominin hand-axes, late Palaeolithic figurines, Neolithic stone arrowheads, Bronze Age ceramics, and historical-period houses. Bayesian methods have also been employed by archaeologists in an attempt to quantify uncertainty in
784-594: A small group of taxa to represent the evolutionary history of its broader population. This process is also known as stratified sampling or clade-based sampling. The practice occurs given limited resources to compare and analyze every species within a target population. Based on the representative group selected, the construction and accuracy of phylogenetic trees vary, which impacts derived phylogenetic inferences. Unavailable datasets, such as an organism's incomplete DNA and protein amino acid sequences in genomic databases, directly restrict taxonomic sampling. Consequently,
840-592: A species to uncover either a higher abundance of important bioactive compounds (e.g., species of Taxus for taxol) or natural variants of known pharmaceuticals (e.g., species of Catharanthus for different forms of vincristine or vinblastine). Phylogenetic analysis has also been applied to biodiversity studies within the fungi family. Phylogenetic analysis helps understand the evolutionary history of various groups of organisms, identify relationships between different species, and predict future evolutionary changes. Emerging imagery systems and new analysis techniques allow for
896-550: Is "tree shape." These approaches, while computationally intensive, have the potential to provide valuable insights into pathogen transmission dynamics. The structure of the host contact network significantly impacts the dynamics of outbreaks, and management strategies rely on understanding these transmission patterns. Pathogen genomes spreading through different contact network structures, such as chains, homogeneous networks, or networks with super-spreaders, accumulate mutations in distinct patterns, resulting in noticeable differences in
952-623: Is a correlation between day-care attendance and contraction of Brazilian Purpuric Fever. Because children are the main victims of BPF, it is assumed that day care facilities may serve as settings for the transmission of H. influenzae biogroup aegyptius conjunctivitis. For a long time, H. aegyptius has been known to cause seasonal epidemics of acute purulent conjunctivitis (minor cases of pink eye). The harsher effects of Hemophilus aegyptius that typically manifest themselves in Brazilian Purpuric Fever are typically seen during
1008-432: Is an excellent Haemophilus growth medium, as it allows for increased accessibility to these factors. Alternatively, Haemophilus is sometimes cultured using the "Staph streak" technique: both Staphylococcus and Haemophilus organisms are cultured together on a single blood agar plate. In this case, Haemophilus colonies will frequently grow in small "satellite" colonies around the larger Staphylococcus colonies because
1064-437: Is the identification, naming, and classification of organisms. Compared to systemization, classification emphasizes whether a species has characteristics of a taxonomic group. The Linnaean classification system developed in the 1700s by Carolus Linnaeus is the foundation for modern classification methods. Linnaean classification relies on an organism's phenotype or physical characteristics to group and organize species. With
1120-590: Is worldwide. Weeks observed that acute conjunctivitis had been observed in Egypt, France, and England. In 1941, Monteiro Salles reported epidemics of H. aegyptius conjunctivitis in Campinas, Sao Paulo State, Brazil. H. aegyptius conjunctivitis has also been observed in the southern states of the United States [Pittman]. The BPF clone of H. influenzae biogroup aegyptius is more difficult to evaluate. Cases of Brazilian Purpuric Fever have been predominant in
1176-428: The evolutionary history of life using genetics, which is known as phylogenetic inference . It establishes the relationship between organisms with the empirical data and observed heritable traits of DNA sequences, protein amino acid sequences, and morphology . The results are a phylogenetic tree —a diagram setting the hypothetical relationships between organisms and their evolutionary history. The tips of
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#17327727755851232-445: The salivary microbiome . Most members of the genus Haemophilus require at least one of these blood factors for growth: hemin (sometimes called 'X-factor') and/or nicotinamide adenine dinucleotide (NAD; sometimes called 'V-factor'); they usually will not grow on blood agar plates. While NAD is released into blood agar by red blood cells, hemin is bound to the blood cells and is unavailable to bacteria in this medium which prevents
1288-602: The BPF clone, more studies should be done before this antibiotic is applied to more cases. Premature use of this antibiotic without further studies (and the use of rifampin to treat sporadic cases) could result in a potential development of resistance and excessive expenses. It is important to distinguish between H. influenzae biogroup aegyptius and the clone referred to as the “BPF clone.” The non-clone, typical version of H. aegyptius manifests itself in non-invasive conjunctivitis. The epidemic nature of this bacteria has been seen in
1344-558: The German Phylogenie , introduced by Haeckel in 1866, and the Darwinian approach to classification became known as the "phyletic" approach. It can be traced back to Aristotle , who wrote in his Posterior Analytics , "We may assume the superiority ceteris paribus [other things being equal] of the demonstration which derives from fewer postulates or hypotheses." The modern concept of phylogenetics evolved primarily as
1400-598: The Sao Paulo state. Sao Paulo is one of the most developed states in Brazil, which makes it easier to receive reports of outbreaks of diseases like BPF. However, it is difficult to know whether BPF has affected other, more rural areas of Brazil. Scientists have not yet determined to what extent BPF has affected rural communities because of a lack of communication technology in these areas and a general lack of medical services. A small case study in Serrana has suggested that there
1456-645: The absence of genetic recombination . Phylogenetics can also aid in drug design and discovery. Phylogenetics allows scientists to organize species and can show which species are likely to have inherited particular traits that are medically useful, such as producing biologically active compounds - those that have effects on the human body. For example, in drug discovery, venom -producing animals are particularly useful. Venoms from these animals produce several important drugs, e.g., ACE inhibitors and Prialt ( Ziconotide ). To find new venoms, scientists turn to phylogenetics to screen for closely related species that may have
1512-414: The basis of a computational classifier used to analyze real-world outbreaks. Computational predictions of transmission dynamics for each outbreak often align with known epidemiological data. Different transmission networks result in quantitatively different tree shapes. To determine whether tree shapes captured information about underlying disease transmission patterns, researchers simulated the evolution of
1568-436: The branching pattern and "degree of difference" to find a compromise between them. Usual methods of phylogenetic inference involve computational approaches implementing the optimality criteria and methods of parsimony , maximum likelihood (ML), and MCMC -based Bayesian inference . All these depend upon an implicit or explicit mathematical model describing the evolution of characters observed. Phenetics , popular in
1624-460: The characteristics of species to interpret their evolutionary relationships and origins. Phylogenetics focuses on whether the characteristics of a species reinforce a phylogenetic inference that it diverged from the most recent common ancestor of a taxonomic group. In the field of cancer research, phylogenetics can be used to study the clonal evolution of tumors and molecular chronology , predicting and showing how cell populations vary throughout
1680-400: The correctness of phylogenetic trees generated using fewer taxa and more sites per taxon on the x-axis to more taxa and fewer sites per taxon on the y-axis. With fewer taxa, more genes are sampled amongst the taxonomic group; in comparison, with more taxa added to the taxonomic sampling group, fewer genes are sampled. Each method has the same total number of nucleotide sites sampled. Furthermore,
1736-413: The data distribution. They may be used to quickly identify differences or similarities in the transmission data. Phylogenetic tools and representations (trees and networks) can also be applied to philology , the study of the evolution of oral languages and written text and manuscripts, such as in the field of quantitative comparative linguistics . Computational phylogenetics can be used to investigate
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1792-426: The direction of inferred evolutionary transformations. In addition to their use for inferring phylogenetic patterns among taxa, phylogenetic analyses are often employed to represent relationships among genes or individual organisms. Such uses have become central to understanding biodiversity , evolution, ecology , and genomes . Phylogenetics is a component of systematics that uses similarities and differences of
1848-597: The discovery of more genetic relationships in biodiverse fields, which can aid in conservation efforts by identifying rare species that could benefit ecosystems globally. Whole-genome sequence data from outbreaks or epidemics of infectious diseases can provide important insights into transmission dynamics and inform public health strategies. Traditionally, studies have combined genomic and epidemiological data to reconstruct transmission events. However, recent research has explored deducing transmission patterns solely from genomic data using phylodynamics , which involves analyzing
1904-523: The disease it was causing; Weeks’ paper called it “the bacillus of acute conjunctival catarrh.” In 1889, in the first classification treatise naming bacteria under the Latin binomial system, Trevisan listed it as “ Bacillus aegyptius .” In the United States, it was listed in 1923 in Bergey’s Manual of Determinative Bacteriology as “ Hemophilus conjuntivitidis .” It was listed as “ Hemophilus aegyptius ” for
1960-488: The dotted line represents a 1:1 accuracy between the two sampling methods. As seen in the graphic, most of the plotted points are located below the dotted line, which indicates gravitation toward increased accuracy when sampling fewer taxa with more sites per taxon. The research performed utilizes four different phylogenetic tree construction models to verify the theory; neighbor-joining (NJ), minimum evolution (ME), unweighted maximum parsimony (MP), and maximum likelihood (ML). In
2016-668: The emergence of biochemistry , organism classifications are now usually based on phylogenetic data, and many systematists contend that only monophyletic taxa should be recognized as named groups. The degree to which classification depends on inferred evolutionary history differs depending on the school of taxonomy: phenetics ignores phylogenetic speculation altogether, trying to represent the similarity between organisms instead; cladistics (phylogenetic systematics) tries to reflect phylogeny in its classifications by only recognizing groups based on shared, derived characters ( synapomorphies ); evolutionary taxonomy tries to take into account both
2072-485: The first time in the seventh edition of Bergey’s Manual after Pittman and Davis explored and described the characteristic differences between this bacterium and H. influenzae . In 1892, Pfeiffer discovered H. influenzae , raising some confusion over whether H. aegyptius was different from H. influenzae . Debate has occurred for more than a century. Pittman, who first gave this bacteria its modern name, felt that these bacteria had enough dissimilarities to be considered
2128-485: The growth of many Haemophilus species. They are unable to synthesize important parts of the cytochrome system needed for respiration, and they obtain these substances from the heme fraction of blood hemoglobin. Clinical laboratories use tests for the hemin and NAD requirement to identify the isolates as Haemophilus species. The species Haemophilus haemoglobinophilus is an exception to this, as it has been shown to grow well on both blood and chocolate agars. Chocolate agar
2184-457: The high frequency of “control” subjects from the affected areas of Brazil that have or had recently had conjunctivitis. These control subjects did not develop Brazilian Purpuric Fever, and therefore were probably not carrying the more dangerous BPF clone of H. influenzae biogroup aegyptius. Affected patients who had recently had conjunctivitis developed a fever and other symptoms of BPF within 1 to 60 days. Historical distribution of H. aegyptius
2240-475: The majority of models, sampling fewer taxon with more sites per taxon demonstrated higher accuracy. Generally, with the alignment of a relatively equal number of total nucleotide sites, sampling more genes per taxon has higher bootstrapping replicability than sampling more taxa. However, unbalanced datasets within genomic databases make increasing the gene comparison per taxon in uncommonly sampled organisms increasingly difficult. The term "phylogeny" derives from
2296-411: The metabolism of Staphylococcus produces the necessary blood factor byproducts required for Haemophilus growth. Haemophilus aegyptius Haemophilus influenzae biogroup aegyptius ( Hae ) is a causative agent of acute and often purulent conjunctivitis , more commonly known as pink eye. It was discovered independently by Koch and Weeks in the 1880s. During the mid-1980s to early 1990s,
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2352-621: The mid-20th century but now largely obsolete, used distance matrix -based methods to construct trees based on overall similarity in morphology or similar observable traits (i.e. in the phenotype or the overall similarity of DNA , not the DNA sequence ), which was often assumed to approximate phylogenetic relationships. Prior to 1950, phylogenetic inferences were generally presented as narrative scenarios. Such methods are often ambiguous and lack explicit criteria for evaluating alternative hypotheses. In phylogenetic analysis, taxon sampling selects
2408-528: The phylogenetic history of a species cannot be read directly from its ontogeny, as Haeckel thought would be possible, but characters from ontogeny can be (and have been) used as data for phylogenetic analyses; the more closely related two species are, the more apomorphies their embryos share. One use of phylogenetic analysis involves the pharmacological examination of closely related groups of organisms. Advances in cladistics analysis through faster computer programs and improved molecular techniques have increased
2464-516: The precision of phylogenetic determination, allowing for the identification of species with pharmacological potential. Historically, phylogenetic screens for pharmacological purposes were used in a basic manner, such as studying the Apocynaceae family of plants, which includes alkaloid-producing species like Catharanthus , known for producing vincristine , an antileukemia drug. Modern techniques now enable researchers to study close relatives of
2520-415: The progression of the disease and during treatment, using whole genome sequencing techniques. The evolutionary processes behind cancer progression are quite different from those in most species and are important to phylogenetic inference; these differences manifest in several areas: the types of aberrations that occur, the rates of mutation , the high heterogeneity (variability) of tumor cell subclones, and
2576-418: The properties of pathogen phylogenies. Phylodynamics uses theoretical models to compare predicted branch lengths with actual branch lengths in phylogenies to infer transmission patterns. Additionally, coalescent theory , which describes probability distributions on trees based on population size, has been adapted for epidemiological purposes. Another source of information within phylogenies that has been explored
2632-455: The recognition of BPF is about 70%. The case definition of Brazilian Purpuric Fever is as follows: H. influenzae biogroup aegyptius is currently susceptible to a number of antibiotics . These include ampicillin, chloramphenicol, amoxicillin-clavulanic acid, cefamandole, cefuroxime, cefotaxime, tetracycline, ceftriaxone and rifampin. Health officials are hesitant in using systemic antibiotics like rifampin. Although they may help in treating
2688-543: The relationship between two variables in pathogen transmission analysis, such as the number of infected individuals and the time since infection. These plots can help identify trends and patterns, such as whether the spread of the pathogen is increasing or decreasing over time, and can highlight potential transmission routes or super-spreader events. Box plots displaying the range, median, quartiles, and potential outliers datasets can also be valuable for analyzing pathogen transmission data, helping to identify important features in
2744-410: The relationships between several of the languages in a timeline, as well as the similarity between words and word order. There are three types of criticisms about using phylogenetics in philology, the first arguing that languages and species are different entities, therefore you can not use the same methods to study both. The second being how phylogenetic methods are being applied to linguistic data. And
2800-578: The relationships between viruses e.g., all viruses are descendants of Virus A. HIV forensics uses phylogenetic analysis to track the differences in HIV genes and determine the relatedness of two samples. Phylogenetic analysis has been used in criminal trials to exonerate or hold individuals. HIV forensics does have its limitations, i.e., it cannot be the sole proof of transmission between individuals and phylogenetic analysis which shows transmission relatedness does not indicate direction of transmission. Taxonomy
2856-485: The same useful traits. The phylogenetic tree shows which species of fish have an origin of venom, and related fish they may contain the trait. Using this approach in studying venomous fish, biologists are able to identify the fish species that may be venomous. Biologist have used this approach in many species such as snakes and lizards. In forensic science , phylogenetic tools are useful to assess DNA evidence for court cases. The simple phylogenetic tree of viruses A-E shows
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#17327727755852912-484: The shape of phylogenetic trees, as illustrated in Fig. 1. Researchers have analyzed the structural characteristics of phylogenetic trees generated from simulated bacterial genome evolution across multiple types of contact networks. By examining simple topological properties of these trees, researchers can classify them into chain-like, homogeneous, or super-spreading dynamics, revealing transmission patterns. These properties form
2968-459: The summer months with few cases of BPF reported during the winter months. Bengtson, while studying H. aegyptius in Georgia, reported that the majority of cases of acute conjunctivitis occurred during the breeding season of the eye gnat, Hippelates pusio . Phylogenetically In biology , phylogenetics ( / ˌ f aɪ l oʊ dʒ ə ˈ n ɛ t ɪ k s , - l ə -/ ) is the study of
3024-421: The third, discusses the types of data that is being used to construct the trees. Bayesian phylogenetic methods, which are sensitive to how treelike the data is, allow for the reconstruction of relationships among languages, locally and globally. The main two reasons for the use of Bayesian phylogenetics are that (1) diverse scenarios can be included in calculations and (2) the output is a sample of trees and not
3080-512: The wide range of shapes they occasionally assume. These organisms inhabit the mucous membranes of the upper respiratory tract, mouth, vagina, and intestinal tract. The genus includes commensal organisms along with some significant pathogenic species such as H. influenzae —a cause of sepsis and bacterial meningitis in young children—and H. ducreyi , the causative agent of chancroid . All members are either aerobic or facultatively anaerobic . This genus has been found to be part of
3136-437: Was caused by two bacteria. The first, and more serious strain was caused by a “gonococcus-like organism.” H. aegyptius was the more benign form, however at this point it had not been named. Three years later, Weeks published a paper detailing the essential characteristics of H. aegyptius (see “Characteristics” section below). Neither Koch nor Weeks gave a name for this bacterium, choosing instead to refer to it in relation to
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