Emerging diversity and ongoing expansion of the genus Brucella

Remarkable genetic diversity and breadth of host species has been uncovered in the Brucella genus over the past decade, fundamentally changing our concept of what it means to be a Brucella. From ocean fishes and marine mammals, to pond dwelling amphibians, forest foxes, desert rodents, and cave-dwelling bats, Brucella have revealed a variety of previously unknown niches. Classical microbiological techniques have been able to help us classify many of these new strains but at times have limited our ability to see the true relationships among or within species. The closest relatives of Brucella are soil bacteria and the adaptations of Brucella spp. to live intracellularly suggest that the genus has evolved to live in vertebrate hosts. Several recently discovered species appear to have phenotypes that are intermediate between soil bacteria and core Brucella, suggesting that they may represent ancestral traits that were subsequently lost in the traditional species. Remarkably, the broad relationships among Brucella species using a variety of sequence and fragment-based approaches have been upheld when using comparative genomics with whole genomes. Nonetheless, genomes are required for fine-scale resolution of many of the relationships and for understanding the evolutionary history of the genus. We expect that the coming decades will reveal many more hosts and previously unknown diversity in a wide range of environments.     

Genomic insights into Brucella

Brucellosis is a zoonotic disease caused by certain species of Brucella. Each species has its preferred host animal, though it can infect other animals too. For a longer period, only six classical species were recognized in the genus Brucella. No vaccine is available for human brucellosis. Therefore, human brucellosis can be controlled only by controlling brucellosis in animals. The genus is now expanding with the newly isolated atypical strains from various animals, including marine mammals. Presently, 12 species of Brucella have been recognized. The first genome of Brucella was released in 2002, and today, we have more than 1500 genomes of Brucella spp. isolated worldwide. Multiple genome sequences are available for the major zoonotic species, B. abortus, B. melitensis, and B. suis. The Brucella genome has two chromosomes with the approximate sizes of 2.1 and 1.2 Mbp. The genome of Brucella is highly conserved across all the species at the nucleotide level. One of the unanswered questions is what makes host preference in different species of Brucella. Here, I summarize the recent advancements in the Brucella genomics research.     

The biological stability of the genus Brucella

The constancy of the three species of Brucella (Br. abortus, Br. suis and Br. melitensis) is discussed with regard to both the historical background and current research, and the pertinent literature is reviewed and interpreted. The authors maintain that members of the genus Brucella are not labile nor are they subject to spontaneous species alteration; stability of the recognized species is confirmed when test reactions used in speciation are standardized and controlled. Particular stress is laid on the epidemiological value of retaining the original species designations. The conclusion that Brucella species are biologically stable is substantiated by the authors'' combined experience of more than 30 years in the isolation and typing of Brucella derived from a variety of sources.     

Molecular taxonomy,phylogeny and biogeography of nematodes belonging to the Trichinella genus

Studying parasites of the genus Trichinella provides scientists of today many advantages. This is a group of zoonotic nematodes that circulates freely among wildlife hosts with one in particular, Trichinella spiralis that is exceptionally well adapted to domestic swine. Recent reports suggest that human infections from hunted animals are on the rise worldwide and numerous countries still experience problems with T. spiralis in their domestic food supplies. Trichinella is a genus whose members are easily propagated in the laboratories, have been used as models to investigate host–parasite relationships and parasitism among clade I organisms, and represent a poorly investigated link between the phylum Nematoda and other Metazoans. The importance of T. spiralis in better understanding the tree of life was so recognized that in 2004, its genome was carefully selected as one of only nine key non-mammalian organisms to be sequenced to completion. Since it was first discovered in 1835, this genus has expanded from being monospecific to eight species including four other genotypes of undetermined taxonomic rank. Inasmuch as discriminating morphological data have been scant, our understanding of the genus has been relegated to a compilation of molecular, biochemical and biological data. Herein, we provide a collection of information and up-to-date interpretations on the taxonomy, diagnostics, systematics, micro- and macroevolution, and the biogeographical and biohistorical reconstruction of the genus Trichinella.     

Examination of two bacterial strains designated `Brucella suis biotype 5'

The morphological, cultural, biochemical, serological and pathogenic properties of two bacterial strains of the group designated `Br. suis biotype 5'' were examined. Both strains were found to be atypical of the genus Brucella in many of these characteristics. No serological relationship to known brucella strains could be detected. On the basis of the evidence obtained the two strains examined were classified as Moraxella duplex and the status of `Br. suis biotype 5'' questioned.     

Delta-pgm,a new live-attenuated vaccine against Brucella suis

Brucellosis is one of the most widespread zoonosis in the world affecting many domestic and wild animals including bovines, goats, pigs and dogs. Each species of the Brucella genus has a particular tropism toward different mammals being the most relevant for human health Brucella abortus, Brucella melitensis and Brucella suis that infect bovines, goats/camelids and swine respectively. Although for B. abortus and B. melitensis there are vaccines available, there is no efficient vaccine to protect swine from B. suis infection so far. We describe here the construction of a novel vaccine strain that confers excellent protection against B. suis in a mouse model of infection. This strain is a clean deletion of the phosphoglucomutase (pgm) gene that codes for a protein that catalyzes the conversion of glucose-6-P to glucose-1-P, which is used as a precursor for the biosynthesis of many polysaccharides. The Delta-pgm strain lacks a complete lipopolysaccharide, is unable to synthesize cyclic beta glucans and is sensitive to several detergents and Polymyxin B. We show that this strain replicates in cultured cells, is completely avirulent in the mouse model of infection but protects against a challenge of the virulent strain inducing the production of pro-inflammatory cytokines. This novel strain could be an excellent candidate for the control of swine brucellosis, a disease of emerging concern in many parts of the world.     

Culicoides Latreille (Diptera: Ceratopogonidae) taxonomy: Current challenges and future directions

Culicoides Latreille biting midges (Diptera: Ceratopogonidae) cause a significant biting nuisance to humans, livestock and equines, and are the biological vectors of a range of internationally important pathogens of both veterinary and medical importance. Despite their economic significance, the delimitation and identification of species and evolutionary relationships between species within this genus remains at best problematic. To date no phylogenetic study has attempted to validate the subgeneric classification of the genus and the monophyly of many of the subgenera remains doubtful. Many informal species groupings are also known to exist but few are adequately described, further complicating accurate identification. Recent contributions to Culicoides taxonomy at the species level have revealed a high correlation between morphological and molecular analyses although molecular analyses are revealing the existence of cryptic species. This review considers the methods for studying the systematics of Culicoides using both morphological and genetic techniques, with a view to understanding the factors limiting our current understanding of Culicoides biology and hence arbovirus epidemiology. In addition, we examine the global status of Culicoides identification, highlighting areas that are poorly addressed, including the potential implementation of emerging technologies.     

Brucella abortus S19 vaccine protects dairy cattle against natural infection with Brucella melitensis

Brucellosis is a zoonotic disease that can cause severe illness in humans and considerable economic loss in the livestock industry. Although small ruminants are the preferential host for Brucella melitensis, this pathogen has emerged as a cause for Brucella outbreaks in cattle. S19 vaccination is implemented in many countries where B. abortus is endemic but its effectiveness against B. melitensis has not been validated. Here we show that vaccine effectiveness in preventing disease transmission between vaccinated and unvaccinated cohorts, as determined by seroconversion, was 87.2% (95% CI 69.5–94.6%). Furthermore, vaccination was associated with a reduced risk for abortion. Together, our data emphasize the role S19 vaccination could play in preventing B. melitensis outbreaks in areas where this pathogen is prevalent in small ruminant populations.     

Historical evolution and current status of the taxonomy of genus Pseudomonas

The genus Pseudomonas was described in 1894 and is one of the most diverse and ubiquitous bacterial genera whose species have been isolated worldwide in all kinds of environments, from the Antarctica to the Tropics, present in sediments, clinical samples, plant, fungi and diseased animal specimens, water, soil, plant rhizosphere, sea, deserts, etc. The taxonomy of the genus has been controversial for years since a lot of bacterial taxa initially included in genus Pseudomonas have been reclassified in other genera or species from a different class of Proteobacteria over the years, as techniques for characterization and classification of microorganisms improved, aiming to set a phylogenetic classification of the species. In this review, the historical evolution of the taxonomy of Pseudomonas is described, and the currently valid criteria and future challenges for taxonomy of the genus and techniques used to achieve the necessary characterization for classifying the species are discussed. Finally, all the validly published Pseudomonas species at present are listed with an overview of their diversity and ecology.     

Evolution of the sequence composition of Flaviviruses

The adaption of pathogens to their host(s) is a major factor in the emergence of infectious disease and the persistent survival of many of the infectious diseases within the population. Since many of the smaller viral pathogens are entirely dependent upon host machinery, it has been postulated that they are under selection for a composition similar to that of their host. Analyses of sequence composition have been conducted for numerous small viral species including the Flavivirus genus. Examination of the species within this particular genus that infect vertebrate hosts revealed that sequence composition proclivities do not correspond with vector transmission as the evolutionary history of this species suggests. Recent sequencing efforts have generated complete genomes for many viral species including members of the Flavivirus genus. A thorough comparison of the sequence composition was conducted for all of the available Flaviviruses for which the complete genome is publicly available. This effort expands the work of previous studies to include new vector-borne species as well as members of the insect-specific group which previously have not been explored. Metrics, including mono-, di-, and tri-nucleotide abundances as well as N_C values and codon usage preferences, were explored both for the entire polyprotein sequence as well as for each individual coding region. Preferences for compositions correspond to host-range rather than evolutionary history; species which infect vertebrate hosts exhibited particular preferences similar to each other as well as in correspondence with their host's preferences. Flaviviruses which do not infect vertebrate hosts, however, did not show these proclivities, with the exception of the Kamiti River virus suggesting its recent (either past or present) infectivity of an unknown vertebrate host.     

Development and evaluation of a core genome multilocus sequence typing (cgMLST) scheme for Brucella spp.

Brucellosis is a zoonotic disease caused by Brucella spp. Brucella spp. can be sub-typed by multilocus sequence typing (MLST) method, which targets a set of housekeeping genes. We have developed a core genome MLST (cgMLST) typing scheme to distinguish and differentiate species of Brucella up to biovar level. A total of 407 whole (complete and draft) genome sequences of different Brucella strains were used in this study. Genome sequences were filtered using the BLAST score ratio (BSR)-based allele calling algorithm, and we found that 164 cgMLST target loci are shared in all the 407 genome sequences. These 164 loci were used to develop the cgMLST scheme and further evaluated to sub-type different species of Brucella. Based on our cgMLST scheme, Brucella spp. were classified into 287 sequence types (STs). A phylogenetic tree was constructed based on the STs derived from the cgMLST analysis. The phylogenetic tree differentiated all the 11 Brucella spp. and five biovars of B. suis. B. vulpis formed the outmost clade followed by B. inopinata and B. microti. Among the four subgroups of B. abortus, group A and B were differentiated based on their geographic origins. Similarly, three subgroups of B. melitensis were separated based on their geographical origins with few exceptions. B. neotomae that infect rodents were distinguished from other Brucella spp. B. canis showed the closest relationship with B. suis bv. 4, followed by B. suis bv. 3 and bv. 1. Brucella spp. associated with the marine mammals, such as B. ceti and B. pinnipedialis were closely related. Of these, B. ceti strains isolated from dolphins and porpoise were differentiated into two groups. We incorporated our cgMLST tool in BrucellaBase (http://www.dbtbrucellosis.in/brucella_cgmlst.html), which will be helpful to predict the cgMLST allelic profile and the ST of a newly sequenced genome.     

Emergence during growth of Brucella strains on dye-agar media of cells that show changes in sulfur metabolism

Division of Brucella strains into three species has long been based on differences in growth characteristics on certain dye-agar media and on variations in H₂S production on liver agar slants. But certain workers believe these differences to be merely quantitative, such as are found between varieties of one species. Moreover, certain strains show characteristics that do not allow them to be classified with certainty in any one of the three species. If all characteristics of one ”species” could be changed in the laboratory so as no longer to be capable of differentiation from those of another, that might be proof that all Brucella strains are in fact varieties of a single species.     

Over-expression of homologous antigens in a leucine auxotroph of Brucella abortus strain RB51 protects mice against a virulent B. suis challenge

Infection by members of the Gram-negative bacterial genus Brucella causes brucellosis in a variety of mammals. Brucellosis in swine remains a challenge, as there is no vaccine in the USA approved for use in swine against brucellosis. Here, we developed an improved recombinant Brucella abortus vaccine strain RB51 that could afford protection against Brucella suis infection by over-expressing genes encoding homologous proteins: L7/L12 ribosomal protein, Cu/Zn superoxide dismutase [SOD] and glycosyl-transferase [WboA]. Using strain RB51leuB as a platform and an antibiotic-resistance marker free plasmid, strains RB51leuB/SOD, RB51leuB/SOD/L7/L12 and RB51leuB/SOD/WboA were constructed to over-express the antigens: SOD alone, SOD and ribosomal protein L7/L12 or SOD and glycosyl-transferase, respectively. The ability of these vaccine candidates to protect against a virulent B. suis challenge were evaluated in a mouse model. All vaccine groups protected mice significantly (P < 0.05) when compared to the control group. Within the vaccine groups, the mice vaccinated with strain RB51leuB/SOD/WboA were significantly better protected than those that were vaccinated with either strain RB51leuB/SOD or RB51leuB/SOD/L7/L12. These results suggest that Brucella antigens can be over-expressed in strain RB51leuB and elicit protective immune responses against brucellosis. Since the plasmid over-expressing homologous antigens does not carry an antibiotic resistance gene, it complies with federal regulations and therefore could be used to develop safer multi-species vaccines for prevention of brucellosis caused by other species of Brucella.     

Safety implication of Salmonella based Brucella vaccine candidate in mice and in vitro human cell culture

An anti-Brucella vaccine candidate comprising rough Salmonella vector delivering Brucella antigens was developed. This system provides a platform for live Brucella-free vaccine development as it can mimic active-intracellular infection of Brucella organism. Exploiting this phenomenon thus provides significant protection at a single dose and also re-assured the safety. To date, no human anti-Brucella vaccines are available, owing to the lack of safe and effective formulation. This study investigated the safety of the vaccine formulation in mice model and in vitro human cell cultures. The experiment was designed to determine the LD50 of the vaccine formulation. The vaccine formulation did not induce any mortality even when mice were administered at 8 × 10⁹ CFU per oral or per subcutaneous (SC), which was 100-times more than the actual vaccine dose intended for mice model. In contrast, wild-type (WT) Salmonella positive control strain induced 100% mortality at 8 × 10⁷ CFU per mice via oral or SC routes. Interaction of the vaccine with phagocytic (THP-1 derived macrophage) and non-phagocytic (Caco-2) human cell lines as well as human PBMC was investigated. In in vitro experiments, inflammatory and pyretic cytokines TNF-α, and IL-1β inductions were significantly lower in vaccine group as compared to WT group. Further, apoptosis, nitric oxide synthase and cytotoxicity inductions were comparable and not exacerbated, given that the strain is based on a rough bacterial vector that may have endotoxic lipid-A more readily exposed. These findings corroborated that the vaccine formulation is highly safe in mice model and is relatively mild in the induction of inflammatory cytokines and cellular changes in human cell lines.     

Genetic diversity of Anaplasma bacteria: Twenty years later

The genus Anaplasma (family Anaplasmataceae, order Rickettsiales) includes obligate intracellular alphaproteobacteria that multiply within membrane-bound vacuoles and are transmitted by Ixodidae ticks to vertebrate hosts. Since the last reclassification of Anaplasmataceae twenty years ago, two new Anaplasma species have been identified. To date, the genus includes eight Anaplasma species (A. phagocytophilum, A. marginale, A. centrale, A. ovis, A. bovis, A. platys, A. odocoilei, and A. capra) and a large number of unclassified genovariants that cannot be assigned to known species. Members of the genus can cause infection in humans and a wide range of domestic animals with different degrees of severity. Long-term persistence which, in some cases, is manifested as cyclic bacteremia has been demonstrated for several Anaplasma species. Zoonotic potential has been shown for A. phagocytophilum, the agent of human granulocytic anaplasmosis, and for some other Anaplasma spp. that suggests a broader medical relevance of this genus. Genetic diversity of Anaplasma spp. has been intensively studied in recent years, and it has been shown that some Anaplasma spp. can be considered as a complex of genetically distinct lineages differing by geography, vectors, and host tropism. The aim of this review was to summarize the current knowledge concerning the natural history, pathogenic properties, and genetic diversity of Anaplasma spp. and some unclassified genovariants with particular attention to their genetic characteristics. The high genetic variability of Anaplasma spp. prompted us to conduct a detailed phylogenetic analysis for different Anaplasma species and unclassified genovariants, which were included in this review. The genotyping of unclassified genovariants has led to the identification of at least four distinct clades that might be considered in future as new candidate species.     

Identification of the causative agents and the epidemiology of porcine brucellosis

Brucella organisms that had been isolated from swine or from human beings exposed to infected swine, and that had been previously identified as members of the species Br. melitensis, were examined for their oxidative metabolism, for their growth patterns on media containing basic fuchsin and thionin, and for their hydrogen sulfide production. These organisms displayed the oxidative metabolic pattern that characterizes and identifies the members of the species Br. suis. They also are identical to Br. suis, type 1, in their tolerance to increased concentrations of thionin in the growth media. They are similar to Br. suis, type 2, in their inability to produce hydrogen sulfide, and share with other members of the species Br. suis the characteristic preference for a porcine host. These findings are evidence that these organisms are not Br. melitensis but are a biotype of Br. suis. Their correct identification is important to understanding the epidemiology of brucellosis.     

Partial protection induced by Salmonella based Brucella vaccine candidate in pregnant guinea pigs

Residual virulence is a major drawback in current Brucella vaccines. Live vaccines induce abortions in pregnant animals. Hence, a novel anti-Brucella vaccine was developed utilizing rough Salmonella delivering four Brucella antigens. Safety implications during pregnancy, humoral immune responses, and protective efficacy against wild type Brucella was investigated in guinea pig model. The vaccine did not induce abortions or severe complications in pregnant guinea pigs when administered 4?×?10⁸?CFU via intraperitoneal route. Systemic IgG determination against antigen components reveals induction of immunity via the Salmonella delivery. Protection efficacy against abortions was 33.3% (2/6) when midterm sow challenged with virulent Brucella 544 strain while none was protected in control group. Lower Brucella recovery in spleen and liver and reduced histopathological burden were also noticed. Although abortion induced by Brucella challenge was not completely prevented, the vaccine candidate may perform better with optimization of vaccination such as inoculation dose optimization.     

Phylogenetic relationships of the Amblyomma cajennense complex (Acari: Ixodidae) at mitogenomic resolution

The genus Amblyomma is the third most diverse in the number of species within the Ixodidae, with practically half of its species distributed in the Americas, though there are also species occurring in Africa, Asia, and Australia. Within the genus, there are several species complexes with veterinary and public health importance. The Amblyomma cajennense complex, in the Americas, is represented by six species with a wide distribution, from Texas to northern Argentina. We combined two sequencing techniques to generate complete mitogenomes of species belonging to the Amblyomma cajennense complex: genome skimming and long-range PCRs sequencing methods. Thus, we generated seven new mitochondrial genomes for all species of the Amblyomma cajennense complex, except for Amblyomma interandinum. Genetic distances between the mitogenomes corroborate the clear differentiation between the five species of the Amblyomma cajennense complex. The phylogenetic relationships of these species had previously been evaluated by combining partial nuclear and mitochondrial genes and here these relationships are corroborated with a more robust framework of data, which demonstrates that the conjunction of mitochondrial and nuclear partial genes can resolve close relationships when entire genes or genomes are unavailable. The gene order, structure, composition, and length are stable across these mitogenomes, and they share the general characteristics of Metastriata. Future studies should increase the number of available mitogenomes for this genus, especially for those species from the Indo-Pacific region and Africa, by means of a better understanding of their relationships and evolutionary process.     

Integrative taxonomy of Mesocriconema onoense (Tylenchida: Criconematidae) from Vietnam highly suggests the synonymization of Mesocriconema brevistylus and related species

The genus Mesocriconema is one of the most diverse genera within the family Criconematidae, known as ring nematodes, with more than 90 species. Although species in this genus usually show distinct morphological characterizations, the identification based only on morphology can lead to misidentification in many studies resulted in a number of synonymizations in the genus over time. In this study, an integrated approach has been applied in characterizing Mesocriconema onoense from Vietnam. The molecular data of 28S rRNA, ITS, 18S rRNA regions were analyzed and discussed to confirm the correct names on GenBank. Besides, phylogenetic analyses of 28S rRNA, ITS, and 18S rRNA regions of Mesocriconema species revealed that Mesocriconema brevistylus should be considered as a junior synonym of M. onoense. Consequently, M. helicus, M. onostris, and M. paronostris should also be considered as the synonyms of M. onoense.     

Morphological and genetic characterization of Syphabulea tjanschani () (Nematoda: Oxyuridae), with phylogenetic position of Syphabulea in Oxyuridae

Pinworms are important parasitic nematodes in animals and humans, and many species are of medical and veterinary importance. The genus Syphabulea is a poorly known group of pinworms. The systematic position of Syphabulea in Oxyuridae remains unclear. Moreover, there is still a paucity of detailed information on some morphological aspects of the type species S. tjanschani (Ablasov, 1962). In the present study, the detailed morphology of S. tjanschani was studied using light microscopy and, for the first time, scanning electron microscopy. The results revealed three traits useful for the characterization of the species including: cuticular depression around excretory pore, non-prominent labial teeth and number of adhesive ridges in three ventral mammelons. The ribosomal [small ribosomal DNA (18S), internal transcribed spacer (ITS) and large ribosomal DNA (28S)] and mitochondrial [cytochrome c oxidase subunit 1 (cox1)] target regions of S. tjanschani were also firstly amplified and sequenced for future use in the molecular identification of this poorly known species. In addition, in order to investigate the systematic position of Syphabulea in Oxyuridae, the phylogenetic analyses of representatives of the Oxyuridae were performed using maximum likelihood (ML) and maximum parsimony (MP) methods based on 18S, 28S and 18S + 28S + cox1 sequence data, respectively. The phylogenetic results based on different sequence data all supported the genus Syphabulea to be a member of the subfamily Syphaciinae. The phylogenetic analysis based on 28S sequence data also showed Syphabulea as sister to the genus Syphatineria. Our present study represents the first attempt to resolve the systematic position of the genus Syphabulea using phylogenetic analyses based on molecular data.