ABSTRACT
In the present article, we report on the identification of Vermamoeba (Hartmannella) vermiformis as the etiological agent of a tissue infection close to the eye of a female patient. Laboratory examination revealed no involvement of any pathogenic bacteria or fungi in the tissue infection. V. vermiformis was identified by cultivation and morphology of trophozoites and cysts as well as phylogenetic analysis of nuclear 18S rDNA. The lesion improved in the course of 4 weeks by application of zinc paste.
Subject(s)
Amebiasis/diagnosis , Amebiasis/pathology , Hartmannella/pathogenicity , Ulcer/parasitology , Adult , Amebiasis/parasitology , Animals , DNA, Protozoan/genetics , DNA, Ribosomal/genetics , Female , Hartmannella/classification , Hartmannella/genetics , Humans , Phylogeny , Trophozoites/classification , Trophozoites/growth & development , Ulcer/pathologyABSTRACT
PURPOSE: To describe the diagnostic and clinical features and treatment results in 43 consecutive patients with microbiologically proven free-living amoebae (FLA) keratitis. METHODS: In this hospital-based, prospective case series, corneal scrapings from 43 patients with presumed amoebic keratitis were plated on nonnutrient agar. Amoebic isolates were identified morphologically and by the polymerase chain reaction. All patients with culture-proven FLA keratitis were treated with polyhexamethylene biguanide (PHMB) 0.02% eye drops. RESULTS: Forty-three corneal scrapings from 43 patients were found to be culture positive for FLA; 41 (95%) were from contact lens wearers and 2 (5%) were from noncontact lens wearers. Microscopic examination identified 4 Acanthamoeba spp, 24 Hartmannella spp, 12 vahlkampfiid amoebae, and 3 mixed infections with Hartmannella/vahlkampfiid amoebae. Morphological results were confirmed by the polymerase chain reaction. Patients with Acanthamoeba, Hartmannella, and vahlkampfiid keratitis had indistinguishable clinical features. In 38 eyes with keratitis at an early stage, treatment with PHMB 0.02% eye drops was fully successful. In 5 patients with advanced keratitis, topical PHMB 0.02% controlled the infection, but all of them developed a central corneal scar with visual deterioration. CONCLUSIONS: Acanthamoeba is not the only cause of amoebic keratitis, because this condition may also be caused by other FLA, such as Hartmannella and vahlkampfiid amoebae. This finding is epidemiologically interesting, suggesting a possible different geographical prevalence of the different FLA responsible for keratitis. Early diagnosis and proper antiamoebic treatment are crucial to yielding a cure.
Subject(s)
Acanthamoeba/isolation & purification , Amebiasis/diagnosis , Amoeba/isolation & purification , Eye Infections, Parasitic/diagnosis , Hartmannella/isolation & purification , Keratitis/diagnosis , Acanthamoeba/genetics , Amebiasis/drug therapy , Amebiasis/parasitology , Amoeba/genetics , Animals , Biguanides/therapeutic use , Cornea/parasitology , DNA Primers/chemistry , DNA, Protozoan/genetics , DNA, Ribosomal/genetics , Disinfectants/therapeutic use , Eye Infections, Parasitic/drug therapy , Eye Infections, Parasitic/parasitology , Female , Hartmannella/genetics , Humans , Keratitis/drug therapy , Keratitis/parasitology , Male , Ophthalmic Solutions , Polymerase Chain Reaction , Prospective Studies , RNA, Ribosomal, 18S/geneticsABSTRACT
Legionella pneumophila proliferates in freshwater environments at temperatures ranging from 25 to 45°C. To investigate the preference of different sequence types (ST) for a specific temperature range, growth of L. pneumophila serogroup 1 (SG1) ST1 (environmental strains), ST47, and ST62 (disease-associated strains) was measured in buffered yeast extract broth (BYEB) and biofilms grown on plasticized polyvinyl chloride in flowing heated drinking water originating from a groundwater supply. The optimum growth temperatures in BYEB were approximately 37°C (ST1), 39°C (ST47), and 41°C (ST62), with maximum growth temperatures of 42°C (ST1) and 43°C (ST47 and ST62). In the biofilm at 38°C, the ST47 and ST62 strains multiplied equally well compared to growth of the environmental ST1 strain and an indigenous L. pneumophila non-SG1 strain, all attaining a concentration of approximately 107 CFU/cm-2 Raising the temperature to 41°C did not impact these levels within 4 weeks, but the colony counts of all strains tested declined (at a specific decline rate of 0.14 to 0.41 day-1) when the temperature was raised to 42°C. At this temperature, the concentration of Vermamoeba vermiformis in the biofilm, determined with quantitative PCR (qPCR), was about 2 log units lower than the concentration at 38°C. In columns operated at a constant temperature, ranging from 38 to 41°C, none of the tested strains multiplied in the biofilm at 41°C, in which also V. vermiformis was not detected. These observations suggest that strains of ST47 and ST62 did not multiply in the biofilm at a temperature of ≥41°C because of the absence of a thermotolerant host. IMPORTANCE: Growth of Legionella pneumophila in tap water installations is a serious public health concern. The organism includes more than 2,100 varieties (sequence types). More than 50% of the reported cases of Legionnaires' disease are caused by a few sequence types which are very rarely detected in the environment. Strains of selected virulent sequence types proliferated in biofilms on surfaces exposed to warm (38°C) tap water to the same level as environmental varieties and multiplied well as pure culture in a nutrient-rich medium at temperatures of 42 and 43°C. However, these organisms did not grow in the biofilms at temperatures of ≥41°C. Typical host amoebae also did not multiply at these temperatures. Apparently, proliferation of thermotolerant host amoebae is needed to enable multiplication of the virulent L. pneumophila strains in the environment at elevated temperatures. The detection of these amoebae in water installations therefore is a scientific challenge with practical implications.
Subject(s)
Biofilms/growth & development , Drinking Water/microbiology , Legionella pneumophila/growth & development , Water Supply , Culture Media/chemistry , Hartmannella/genetics , Hartmannella/growth & development , Hot Temperature , Humans , Legionella pneumophila/classification , Legionella pneumophila/genetics , Legionella pneumophila/physiology , Legionnaires' Disease/microbiology , Real-Time Polymerase Chain Reaction , TemperatureABSTRACT
This study was conducted to determine the presence and molecular identity of Acanthamoeba species in the surface water resources of four provinces in Iran, namely Guilan, Mazandaran (North of Iran), Alborz, and Tehran (capital city), using culture- and molecular-based methods. During March to November 2014, 49 surface water samples were collected from environmental water sources-the distinct surface waters of Guilan, Mazandaran, Alborz, and Tehran provinces, in Iran. For the isolation of Acanthamoeba species, approximately 500 ml of the water samples were filtered through a cellulose nitrate membrane with a pore size of 0.45 µ. The filter was transferred onto non-nutrient agar plates seeded with Gram-negative bacteria (Escherichia coli) as a food source. The presence of Acanthamoeba was confirmed by the genus-specific primer pair JDP1 and 2, and/or NA primers were used to identify Acanthamoeba and certain other free-living amoebae. In total, 38 out of 49 samples were positive by culture and/or PCR for Acanthamoeba and other free-living amoebae from all three provinces. By sequencing the positive isolates, the strains were shown to belong to Acanthamoeba (16 isolates belonged to T4 and 2 isolates belonged to T5), Hartmannella vermiformis (3/24), and Saccamoeba limax (2/24). The T4 and T5 genotypes were detected in Guilan and Mazandaran provinces. Two isolates from Guilan and Tehran provinces belonged to S. limax, and H. vermiformis was detected in Guilan province. The results of this study highlight the need to pay more attention to free-living amoebae, as human activity was observed in all of the localities from which these samples were taken. These surface waters can be potential sources for the distribution and transmission of pathogenic Acanthamoeba in the study areas, and free-living amoebas (FLA) (particularly the Acanthamoeba species) can serve as hosts for and vehicles of various microorganisms.
Subject(s)
Acanthamoeba/isolation & purification , Amoebozoa/isolation & purification , Hartmannella/isolation & purification , Water/parasitology , Acanthamoeba/classification , Acanthamoeba/genetics , Amoebozoa/classification , Amoebozoa/genetics , Hartmannella/classification , Hartmannella/genetics , Human Activities , Humans , Iran , Polymerase Chain Reaction , Water ResourcesABSTRACT
The free-living amoebae (FLA) may live in the environment and also within other organisms as parasites and then they are called amphizoic. They are potentially pathogenic for humans and animals and are found in water that is a source of infection. The aim of this study was molecular detection and identification of these FLA in natural water bodies in North-Western Poland to evaluate the risk of the pathogenic amoebae infections. We examined surface water samples collected from 50 sites and first, the tolerance thermic test was performed in order to select thermophilic, potentially pathogenic strains. For molecular identification of FLA, regions of 18S rDNA, 16S rDNA and intergenic spacers were amplified. Acanthamoeba T4 and T16 genotypes of 18S rDNA gene and 18S rDNA of H. vermiformis were detected. We identified two variants of Acanthamoeba T4 genotype, two variants of Acanthamoeba T16 genotype and one variant of H. vermiformis. Identification of the T16 genotype and H. vermiformis in water was for the first time in Poland. Additionally, we made attempts to adapt the RLB method for detection and differentiation of FLA species and strains. PCR seems to be more sensitive than RLB hybridization, though.
Subject(s)
Acanthamoeba/classification , Amebiasis/parasitology , Genetic Variation , Hartmannella/classification , Acanthamoeba/genetics , Acanthamoeba/isolation & purification , Animals , Base Sequence , DNA, Ribosomal/genetics , DNA, Ribosomal Spacer/genetics , Fresh Water , Genotype , Hartmannella/genetics , Hartmannella/isolation & purification , Humans , Molecular Sequence Data , Poland , Polymerase Chain Reaction , Sequence Analysis, DNA , Species SpecificityABSTRACT
In March 2010, a 35 year-old HIV/AIDS female patient was admitted to hospital to start treatment with Highly Active Antiretroviral Therapy (HAART) since during a routine control a dramatic decrease in the CD4(+) levels was detected. At this stage, a nasal swab from each nostril was collected from the patient to include it in the samples for the case study mentioned above. Moreover, it is important to mention that the patient was diagnosed in 2009 with invasive pneumococcal disease, acute cholecystitis, pancreatitis and pulmonary tuberculosis. The collected nasal swabs from both nostrils were positive for Vermamoeba vermiformis species which was identified using morphological and PCR/DNA sequencing approaches. Basic Local Alignment Search Tool (BLAST) homology and phylogenetic analysis confirmed the amoebic strain to belong to V.vermiformis species. Molecular identification of the Mycobacterium strain was carried out using a bacterial universal primer pair for the 16S rDNA gene at the genus level and the rpoB gene was amplified and sequenced as previously described to identify the Mycobacterium species (Shin et al., 2008; Sheen et al., 2013). Homology and phylogenetic analyses of the rpoB gene confirmed the species as Mycobacterium chelonae. In parallel, collected swabs were tested by PCR and were positive for the presence of V.vermiformis and M.chelonae. This work describes the identification of an emerging bacterial pathogen,M.chelonae from a Free-Living Amoebae (FLA) strain belonging to the species V.vermiformis that colonized the nasal cavities of an HIV/AIDS patient, previously diagnosed with TB. Awareness within clinicians and public health professionals should be raised, as pathogenic agents such as M.chelonae may be using FLA to propagate and survive in the environment.
Subject(s)
Amebiasis/complications , HIV Infections/complications , Hartmannella/microbiology , Mycobacterium Infections, Nontuberculous/complications , Mycobacterium chelonae/isolation & purification , Symbiosis , Adult , DNA, Bacterial/isolation & purification , DNA, Protozoan/isolation & purification , Disease Reservoirs , Female , HIV Infections/microbiology , HIV Infections/parasitology , Hartmannella/genetics , Hartmannella/isolation & purification , Humans , Molecular Sequence Data , Mycobacterium Infections, Nontuberculous/transmission , Mycobacterium chelonae/genetics , Mycobacterium chelonae/physiology , Nasal Mucosa/microbiology , Nasal Mucosa/parasitology , PeruABSTRACT
The present study was aimed at investigating the coexistence and interactions between free living amoebae of Naegleria and Hartmannella genera and pathogenic Legionella pneumophila bacteria in thermal saline baths used in balneotherapy in central Poland. Water samples were collected from November 2010 to May 2011 at intervals longer than 1 month. The microorganisms were detected with the use of a very sensitive fluorescence in situ hybridisation method. In addition, the morphology of the amoebae was studied. Despite relatively high salinity level, ranging from 1.5 to 5.0 %, L. pneumophila were found in all investigated baths, although their number never exceeded 10(6) cells dm(-3). Hartmannella were not detected, while Naegleria fowleri were found in one bath. The observation that N. fowleri and L. pneumophila may coexist in thermal saline baths is the first observation emphasising potential threat from these microorganisms in balneotherapy.
Subject(s)
Balneology/methods , Hartmannella/isolation & purification , Legionella pneumophila/isolation & purification , Naegleria fowleri/isolation & purification , Water Microbiology , Water/parasitology , Baths/methods , Hartmannella/cytology , Hartmannella/genetics , Humans , In Situ Hybridization, Fluorescence , Legionella pneumophila/genetics , Naegleria fowleri/cytology , Naegleria fowleri/genetics , Poland , Salinity , TemperatureABSTRACT
Legionella are commonly found in natural and man-made aquatic environments and are able to inhabit various species of protozoa. The relationship between the occurrence of Legionella spp. within protozoa and human legionellosis has been demonstrated; however, the proportions of intracellular and extracellular Legionella spp. in the aquatic environment were rarely reported. In this study, we developed a new method to differentiate intracellular and extracellular Legionella spp. in the aquatic environment. Water samples from three thermal spring recreational areas in southeastern Taiwan were collected and analyzed. For each water sample, concurrent measurements were performed for Legionella spp. and their free-living amoebae hosts. The overall detection rate was 32 % (16/50) for intracellular Legionella spp. and 12 % (6/50) for extracellular Legionella spp. The most prevalent host of Legionella spp. was Hartmannella vermiformis. The identified Legionella spp. differed substantially between intracellular and extracellular forms. The results showed that it may be necessary to differentiate intracellular and extracellular forms of Legionella spp.
Subject(s)
Bacterial Load/methods , Hot Springs/microbiology , Hot Springs/parasitology , Legionella/classification , Legionella/isolation & purification , Lobosea/microbiology , Acanthamoeba/genetics , Acanthamoeba/isolation & purification , Acanthamoeba/microbiology , Colony Count, Microbial , Hartmannella/genetics , Hartmannella/isolation & purification , Hartmannella/microbiology , Legionella/genetics , Legionella/physiology , Lobosea/genetics , Lobosea/isolation & purification , Naegleria/genetics , Naegleria/isolation & purification , Naegleria/microbiology , Phylogeny , Polymerase Chain Reaction , Sequence Analysis, DNA , Sequence Homology , TaiwanABSTRACT
This study investigated the occurrence of free-living amoebae (FLA) in immunodeficiency wards of hospitals in Tehran, Iran. A total of 70 dust and biofilm samples from wards serving transplant, pediatric (malignancies), HIV, leukemia and oncology patients of five university hospitals were collected and examined for the presence of FLA using culturing and molecular approaches. Based on the morphology of the amoebae in plate cultures, primer sets were applied for molecular identification of Acanthamoeba, vahlkampfiid amoebae and Hartmannella. Out of 70 samples, 37 (52.9%) were positive for FLA. Acanthamoeba belonged to the T4 genotype was the most prevalent isolate. Presence of the T4 genotype on medical instruments, including an oxygen mask in an isolation room of an immunodeficiency pediatric ward, should be of concern for health authorities. Acanthamoeba T5 genotypes, Hartmannella vermiformis, and Vahlkampfia avara were also present. These results highlight a clear need for greater attention to improved disinfection, especially where susceptible patients, such as those who are immune-suppressed, are served. To our knowledge, this is the first report of these FLA in immunodeficiency wards in Iran, and also the first to identify Acanthamoeba T5, Hartmannella, and Vahlkampfia in moist habitats, such as biofilms, in this country.
Subject(s)
Acanthamoeba/isolation & purification , Environmental Microbiology , Hartmannella/isolation & purification , Schizopyrenida/isolation & purification , Acanthamoeba/classification , Acanthamoeba/cytology , Acanthamoeba/genetics , Biofilms , DNA, Protozoan/chemistry , DNA, Protozoan/genetics , DNA, Ribosomal Spacer/chemistry , DNA, Ribosomal Spacer/genetics , Hartmannella/classification , Hartmannella/cytology , Hartmannella/genetics , Hospitals, University , Humans , Immunocompromised Host , Iran , Molecular Sequence Data , Schizopyrenida/classification , Schizopyrenida/cytology , Schizopyrenida/genetics , Sequence Analysis, DNAABSTRACT
Legionella pneumophila proliferates in aquatic habitats within free-living protozoa, 17 species of which have been identified as hosts by using in vitro experiments. The present study aimed at identifying protozoan hosts for L. pneumophila by using a biofilm batch test (BBT). Samples (600 ml) collected from 21 engineered freshwater systems, with added polyethylene cylinders to promote biofilm formation, were inoculated with L. pneumophila and subsequently incubated at 37°C for 20 days. Growth of L. pneumophila was observed in 16 of 18 water types when the host protozoan Hartmannella vermiformis was added. Twelve of the tested water types supported growth of L. pneumophila or indigenous Legionella anisa without added H. vermiformis. In 12 of 19 BBT flasks H. vermiformis was indicated as a host, based on the ratio between maximum concentrations of L. pneumophila and H. vermiformis, determined with quantitative PCR (Q-PCR), and the composition of clone libraries of partial 18S rRNA gene fragments. Analyses of 609 eukaryotic clones from the BBTs revealed that 68 operational taxonomic units (OTUs) showed the highest similarity to free-living protozoa. Forty percent of the sequences clustering with protozoa showed ≥99.5% similarity to H. vermiformis. None of the other protozoa serving as hosts in in vitro studies were detected in the BBTs. In several tests with growth of L. pneumophila, the protozoa Diphylleia rotans, Echinamoeba thermarum, and Neoparamoeba sp. were identified as candidate hosts. In vitro studies are needed to confirm their role as hosts for L. pneumophila. Unidentified protozoa were implicated as hosts for uncultured Legionella spp. grown in BBT flasks at 15°C.
Subject(s)
Biofilms , Hartmannella/microbiology , Legionella pneumophila/physiology , Water Microbiology , Acanthamoeba/genetics , Acanthamoeba/microbiology , Bacteriological Techniques/methods , Base Sequence , DNA, Bacterial/genetics , Hartmannella/genetics , Legionella pneumophila/genetics , Molecular Sequence Data , Polymerase Chain Reaction , RNA, Ribosomal, 16S/genetics , Water SupplyABSTRACT
5S rRNAs are ubiquitous components of prokaryotic, chloroplast, and eukaryotic cytosolic ribosomes but are apparently absent from mitochondrial ribosomes (mitoribosomes) of many eukaryotic groups including animals and fungi. Nevertheless, a clearly identifiable, mitochondrion-encoded 5S rRNA is present in Acanthamoeba castellanii, a member of Amoebozoa. During a search for additional mitochondrial 5S rRNAs, we detected small abundant RNAs in other members of Amoebozoa, namely, in the lobose amoeba Hartmannella vermiformis and in the myxomycete slime mold Physarum polycephalum. These RNAs are encoded by mitochondrial DNA (mtDNA), cosediment with mitoribosomes in glycerol gradients, and can be folded into a secondary structure similar to that of bona fide 5S rRNAs. Further, in the mtDNA of another slime mold, Didymium nigripes, we identified a region that in sequence, potential secondary structure, and genomic location is similar to the corresponding region encoding the Physarum small RNA. A mtDNA-encoded small RNA previously identified in Dictyostelium discoideum is here shown to share several characteristics with known 5S rRNAs. Again, we detected genes encoding potential homologs of this RNA in the mtDNA of three other species of the genus Dictyostelium as well as in a related genus, Polysphondylium. Taken together, our results indicate a widespread occurrence of small, abundant, mtDNA-encoded RNAs with 5S rRNA-like structures that are associated with the mitoribosome in various amoebozoan taxa. Our working hypothesis is that these novel small abundant RNAs represent radically divergent mitochondrial 5S rRNA homologs. We posit that currently unrecognized 5S-like RNAs may exist in other mitochondrial systems in which a conventional 5S rRNA cannot be identified.
Subject(s)
Amoebozoa/genetics , Genome, Mitochondrial/genetics , RNA, Ribosomal, 5S/genetics , Amoebozoa/cytology , Animals , Base Sequence , Cell Fractionation , Computational Biology , Conserved Sequence , DNA, Mitochondrial/genetics , Dictyostelium/genetics , Hartmannella/genetics , Mitochondria/genetics , Molecular Sequence Data , Nucleic Acid Conformation , Phylogeny , Physarum polycephalum/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA, Ribosomal, 5S/chemistry , Ribosome Subunits, Large, Eukaryotic/genetics , Sequence Homology, Amino AcidABSTRACT
Acanthamoeba, Hartmannella, and Naegleria are free-living amoebae, ubiquitous in aquatic environments. Several species within these genera are recognized as potential human pathogens. These free-living amoebae may facilitate the proliferation of their parasitical bacteria, such as Legionella. In this study, we identified Acanthamoeba, Hartmannella, Naegleria, and Legionella using various analytical procedures and investigated their occurrence at a mud spring recreation area in Taiwan. We investigated factors potentially associated with the prevalence of the pathogens, including various water types, and physical and microbiological water quality parameters. Spring water was collected from 34 sites and Acanthamoeba, Hartmannella, Naegleria, and Legionella were detected in 8.8%, 35.3%, 14.7%, and 47.1%, respectively. The identified species of Acanthamoeba included Acanthamoeba castellanii and Acanthamoeba polyphaga. Nearly all the Hartmannella isolates are identified as Hartmannella vermiformis. The Naegleria species included Naegleria australiensis and its sister groups, and two other isolates referred to a new clade of Naegleria genotypes. The Legionella species identified included unnamed Legionella genotypes, Legionella pneumophila serotype 6, uncultured Legionella spp., Legionella lytica, Legionella drancourtii, and Legionella waltersii. Significant differences (Mann-Whitney U test, P<0.05) were observed between the presence/absence of Hartmannella and total coliforms, between the presence/absence of Naegleria and heterotrophic plate counts, and between the presence/absence of Legionella and heterotrophic plate counts. This survey confirms that pathogenic free-living amoebae and Legionella are prevalent in this Taiwanese mud spring recreation area. The presence of pathogens should be considered a potential health threat when associated with human activities in spring water.
Subject(s)
Acanthamoeba/isolation & purification , Hartmannella/isolation & purification , Legionella/isolation & purification , Naegleria/isolation & purification , Soil Microbiology , Water Microbiology , Acanthamoeba/classification , Animals , Hartmannella/classification , Hartmannella/genetics , Legionella/classification , Legionella/genetics , Naegleria/classification , Naegleria/genetics , Phylogeny , RNA, Ribosomal, 18S/genetics , Recreation , Water/parasitologyABSTRACT
From comparative analysis of EST data for five taxa within the eukaryotic supergroup Amoebozoa, including two free-living amoebae (Acanthamoeba castellanii, Hartmannella vermiformis) and three slime molds (Physarum polycephalum, Hyperamoeba dachnaya and Hyperamoeba sp.), we obtained new broad-range perspectives on the evolution and biosynthetic capacity of this assemblage. Together with genome sequences for the amoebozoans Dictyostelium discoideum and Entamoeba histolytica, and including partial genome sequence available for A. castellanii, we used the EST data to identify genes that appear to be exclusive to the supergroup, and to specific clades therein. Many of these genes are likely involved in cell-cell communication or differentiation. In examining on a broad scale a number of characters that previously have been considered in simpler cross-species comparisons, typically between Dictyostelium and Entamoeba, we find that Amoebozoa as a whole exhibits striking variation in the number and distribution of biosynthetic pathways, for example, ones for certain critical stress-response molecules, including trehalose and mannitol. Finally, we report additional compelling cases of lateral gene transfer within Amoebozoa, further emphasizing that although this process has influenced genome evolution in all examined amoebozoan taxa, it has done so to a variable extent.
Subject(s)
Amoebida/genetics , Biodiversity , Expressed Sequence Tags , Genes, Protozoan , Physarum polycephalum/genetics , Acanthamoeba castellanii/genetics , Amoebida/classification , Amoebida/physiology , Animals , Carbohydrate Metabolism , DNA, Protozoan/genetics , Evolution, Molecular , Gene Library , Gene Transfer, Horizontal , Genome, Protozoan , Hartmannella/genetics , Meiosis , Physarum polycephalum/classification , Physarum polycephalum/physiology , Species SpecificityABSTRACT
Single-celled bacterivorous eukaryotes offer excellent test cases for evaluation of the frequency of prey-to-predator lateral gene transfer (LGT). Here we use analysis of expressed sequence tag (EST) data sets to quantify the extent of LGT from eubacteria to two amoebae, Acanthamoeba castellanii and Hartmannella vermiformis. Stringent screening for LGT proceeded in several steps intended to enrich for authentic events while at the same time minimizing the incidence of false positives due to factors such as limitations in database coverage and ancient paralogy. The results were compared with data obtained when the same methodology was applied to EST libraries from a number of other eukaryotic taxa. Significant differences in the extent of apparent eubacterium-to-eukaryote LGT were found between taxa. Our results indicate that there may be substantial inter-taxon variation in the number of LGT events that become fixed even between amoebozoan species that have similar feeding modalities.
Subject(s)
Acanthamoeba castellanii/genetics , Eubacterium/genetics , Gene Transfer, Horizontal , Genetic Variation , Hartmannella/genetics , Phylogeny , Animals , Expressed Sequence TagsABSTRACT
Real-time polymerase chain reaction melting curve analysis (MCA) allows differentiation of several free-living amoebae species. Distinctive characteristics were found for Naegleria fowleri, N. lovaniensis, N. australiensis, N. gruberi, Hartmanella vermiformis, and Willaertia magna. Species specificity of the amplicons was confirmed using agarose gel electrophoresis and sequence-based approaches. Amplification efficiency ranged from 91% to 98%, indicating the quantitative potential of the assay. This MCA approach can be used for quantitative detection of free-living amoebae after cultivation but also as a culture-independent detection method.
Subject(s)
Amoebida/isolation & purification , Naegleria/isolation & purification , Polymerase Chain Reaction/methods , Acanthamoeba castellanii/classification , Acanthamoeba castellanii/genetics , Acanthamoeba castellanii/isolation & purification , Amoebida/classification , Amoebida/genetics , Animals , Hartmannella/classification , Hartmannella/genetics , Hartmannella/isolation & purification , Naegleria/classification , Naegleria/genetics , Sensitivity and Specificity , Species SpecificityABSTRACT
A real-time PCR-based method targeting the 18S rRNA gene was developed for the quantitative detection of Hartmannella vermiformis, a free-living amoeba which is a potential host for Legionella pneumophila in warm water systems and cooling towers. The detection specificity was validated using genomic DNA of the closely related amoeba Hartmannella abertawensis as a negative control and sequence analysis of amplified products from environmental samples. Real-time PCR detection of serially diluted DNA extracted from H. vermiformis was linear for microscopic cell counts between 1.14 x 10(-1) and 1.14 x 10(4) cells per PCR. The genome of H. vermiformis harbors multiple copies of the 18S rRNA gene, and an average number (with standard error) of 1,330 +/- 127 copies per cell was derived from real-time PCR calibration curves for cell suspensions and plasmid DNA. No significant differences were observed between the 18S rRNA gene copy numbers for trophozoites and cysts of strain ATCC 50237 or between the copy numbers for this strain and strain KWR-1. The developed method was applied to water samples (200 ml) collected from a variety of lakes and rivers serving as sources for drinking water production in The Netherlands. Detectable populations were found in 21 of the 28 samples, with concentrations ranging from 5 to 75 cells/liter. A high degree of similarity (> or =98%) was observed between sequences of clones originating from the different surface waters and between these clones and the reference strains. Hence, H. vermiformis, which is highly similar to strains serving as hosts for L. pneumophila, is a common component of the microbial community in fresh surface water.
Subject(s)
Hartmannella/genetics , Hartmannella/isolation & purification , Animals , Base Sequence , DNA Primers/genetics , Gene Dosage , Genes, Protozoan , Hartmannella/microbiology , Legionella pneumophila/isolation & purification , Molecular Sequence Data , Netherlands , Phylogeny , Polymerase Chain Reaction/methods , Polymerase Chain Reaction/statistics & numerical data , RNA, Protozoan/genetics , RNA, Ribosomal, 18S/genetics , Reproducibility of Results , Sensitivity and Specificity , Water/parasitologyABSTRACT
Mitochondrial transcription factor B (mtTFB), an essential component in regulating the expression of mitochondrial DNA-encoded genes in both yeast and humans, is a dimethyladenosine methyltransferase (DMT) that has acquired a secondary role in mitochondrial transcription. So far, mtTFB has only been well studied in Opisthokonta (metazoan animals and fungi). Here we investigate the phylogenetic distribution of mtTFB homologs throughout the domain Eucarya, documenting the first examples of this protein outside of the opisthokonts. Surprisingly, we identified putative mtTFB homologs only in amoebozoan protists and trypanosomatids. Phylogenetic analysis together with conservation of intron positions in amoebozoan and human genes supports the grouping of the putative mtTFB homologs as a distinct clade. Phylogenetic analysis further demonstrates that the mtTFB is most likely derived from the DMT of the mitochondrial endosymbiont.
Subject(s)
Eukaryota/genetics , Evolution, Molecular , Mitochondria/genetics , Mitochondrial Proteins/genetics , Transcription Factors/genetics , Acanthamoeba castellanii/genetics , Alphaproteobacteria/genetics , Amino Acid Sequence , Animals , DNA-Binding Proteins/genetics , Dictyostelium/genetics , Eukaryotic Cells , Hartmannella/genetics , Humans , Introns , Molecular Sequence Data , Phylogeny , Sequence Homology, Nucleic Acid , SymbiosisABSTRACT
Cochliopodium is a very distinctive genus of discoid amoebae covered by a dorsal tectum of carbohydrate microscales. Its phylogenetic position is unclear, since although sharing many features with naked "gymnamoebae", the tectum sets it apart. We sequenced 18S ribosomal RNA genes from three Cochliopodium species (minus, spiniferum and Cochliopodium sp., a new species resembling C. minutum). Phylogenetic analysis shows Cochliopodium as robustly holophyletic and within Amoebozoa, in full accord with morphological data. Cochliopodium is always one of the basal branches within Amoebozoa but its precise position is unstable. In Bayesian analysis it is sister to holophyletic Glycostylida, but distance trees mostly place it between Dermamoeba and a possibly artifactual long-branch cluster including Thecamoeba. These positions are poorly supported and basal amoebozoan branching ill-resolved, making it unclear whether Discosea (Glycostylida, Himatismenida, Dermamoebida) is holophyletic; however, Thecamoeba seems not specifically related to Dermamoeba. We also sequenced the small-subunit rRNA gene of Vannella persistens, which constantly grouped with other Vannella species, and two Hartmannella strains. Our trees suggest that Vexilliferidae, Variosea and Hartmannella are polyphyletic, confirming the existence of two very distinct Hartmannella clades: that comprising H. cantabrigiensis and another divergent species is sister to Glaeseria, whilst Hartmannella vermiformis branches more deeply.
Subject(s)
Eukaryota/classification , RNA, Ribosomal, 18S/genetics , Animals , Base Sequence , DNA, Protozoan/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Eukaryota/genetics , Hartmannella/genetics , Lobosea/classification , Lobosea/genetics , Molecular Sequence Data , PhylogenyABSTRACT
Based on morphological and molecular characterisation, four amoeba strains isolated from organs of freshwater fish were identified as Hartmannella vermiformis Page, 1967. Small subunit rRNA gene sequences of these strains expand the set of corresponding complete and almost complete sequences of this species to twelve. A new species-specific oligonucleotide probe inferred from recently available SSU rRNA gene sequences was designed and successfully tested in tissue lesions produced by one strain of H. vermiformis in experimentally infected fish.