Geographic origin and spread of pathogenic Naegleria fowleri deduced from restriction enzyme patterns of repeated DNA

Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers

Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.

Identifying endosymbiont bacteria associated with free-living amoebae

The association between free-living amoebae and pathogenic bacteria is an issue that has gained great importance due to the environmental and health consequences that it implies. In this paper, we analyse the techniques to follow an epidemiological study to identify associations between genera, species, genotypes and subgenotypes of amoebae with pathogenic bacteria, analysing their evolution and considering their usefulness. In this sense, we highlight the combination of microscopic and molecular techniques as the most appropriate way to obtain fully reliable results as well as the need to achieve the standardization of these techniques to allow the comparison of both environmental and clinical results.

Origin and evolution of the worldwide distributed pathogenic amoeboflagellate Naegleria fowleri

Naegleria fowleri, a worldwide distributed pathogen, is the causative agent of primary amoebic meningoencephalitis. Because it is such a fulminant disease, most patients do not survive the infection. This pathogen is a free-living amoeboflagellate present in warm water. To date, it is well established that there are several types of N. fowleri, which can be distinguished based on the length of the internal transcribed spacer 1 and a one bp transition in the 5.8S rDNA. Seven of the eight known types have been detected in Europe. Three types are present in the USA, of which one is unique to this country. Only one of the eight types occurs in Oceania (Australia and New Zealand) and Japan. In mainland Asia (India, China and Thailand) the two most common types are found, which are also present in Europe and the USA. There is strong indication that the pathogenic N. fowleri evolved from the nonpathogenic Naegleria lovaniensis on the American continent. There is no evidence of virulence differences between the types of N. fowleri. Two other Naegleria spp. are pathogenic for mice, but human infections due to these two other Naegleria spp. are not known.

Free-living amoebae as opportunistic and non-opportunistic pathogens of humans and animals

Knowledge that free-living amoebae are capable of causing human disease dates back some 50 years, prior to which time they were regarded as harmless soil organisms or, at most, commensals of mammals. First Naegleria fowleri, then Acanthamoeba spp. and Balamuthia mandrillaris, and finally Sappinia diploidea have been recognised as etiologic agents of encephalitis; Acanthamoeba spp. are also responsible for amoebic keratitis. Some of the infections are opportunistic, occurring mainly in immunocompromised hosts (Acanthamoeba and Balamuthia encephalitides), while others are non-opportunistic (Acanthamoeba keratitis, Naegleria meningoencephalitis, and cases of Balamuthia encephalitis occurring in immunocompetent humans). The amoebae have a cosmopolitan distribution in soil and water, providing multiple opportunities for contacts with humans and animals, as evidenced by antibody titers in surveyed human populations. Although, the numbers of infections caused by these amoebae are low in comparison to other protozoal parasitoses (trypanosomiasis, toxoplasmosis, malaria, etc.), the difficulty in diagnosing them, the challenge of finding optimal antimicrobial treatments and the morbidity and relatively high mortality associated with, in particular, the encephalitides have been a cause for concern for clinical and laboratory personnel and parasitologists. This review presents information about the individual amoebae: their morphologies and life-cycles, laboratory cultivation, ecology, epidemiology, nature of the infections and appropriate antimicrobial therapies, the immune response, and molecular diagnostic procedures that have been developed for identification of the amoebae in the environment and in clinical specimens.

Genetic variations in the internal transcribed spacer and mitochondrial small subunit rRNA gene of Naegleria spp

Naegleria spp. are widely distributed free-living amebas, but one species in the genus, N. fowleri, causes acute fulminant primary amebic meningoencephalitis in humans and other animals. Thus, it is important to differentiate N. fowleri from the rest in the genus of Naegleria, and to develop tools for the detection of intra-specific genetic variations. In this study, one isolate each of N. australiensis, N. gruberi, N. jadini, and N. lovaniensis and 22 isolates of N. fowleri were characterized at the internal transcribed spacers (ITS) and mitochondrial small subunit rRNA (mtSSU rRNA) gene. The mtSSU rRNA primers designed amplified DNA of all isolates, with distinct sequences obtained from all species examined. In contrast, the ITS primers only amplified DNA from N. lovaniensis and N. fowleri, with minor sequence differences between the two. Three genotypes of N. fowleri were found among the isolates analyzed in both the mtSSU rRNA gene and ITS. The extent of sequence variation was greater in the mtSSU rRNA gene, but the ITS had the advantage of length polymorphism. These data should be useful in the development of molecular tools for rapid species differentiation and genotyping of Naegleria spp.

Genetic variation in the free-living amoeba Naegleria fowleri

In this study, 30 strains of the pathogenic free-living amoeba Naegleria fowleri were investigated by using the randomly amplified polymorphic DNA (RAPD) method. The present study confirmed our previous finding that RAPD variation is not correlated with geographical origin. In particular, Mexican strains belong to the variant previously detected in Asia, Europe, and the United States. In France, surprisingly, strains from Cattenom gave RAPD patterns identical to those of the Japanese strains. In addition, all of these strains, together with an additional French strain from Chooz, exhibited similarities to South Pacific strains. The results also confirmed the presence of numerous variants in Europe, whereas only two variants were detected in the United States. The two variants found in the United States were different from the South Pacific variants. These findings do not support the previous hypothesis concerning the origin and modes of dispersal of N. fowleri.

Development of a PCR for identification of Naegleria fowleri from the environment

A species-specific PCR for the identification of Naegleria fowleri was developed. In sensitivity studies, 10 trophozoites or cysts and 1 trophozoite or cyst could be detected after 35 and 45 cycles, respectively. In conjunction with a rapid DNA isolation method, this PCR was used to identify N. fowleri directly from primary cultures of environmental samples.

Identification and epidemiological typing of Naegleria fowleri with DNA probes

Naegleria fowleri is a small free-living amoeboflagellate found in warm water habitats worldwide. The organism is pathogenic to humans, causing fatal primary amoebic meningoencephalitis. When monitoring the environment for the presence of N. fowleri, it is important to reliably differentiate the organism from other closely related but nonpathogenic species. To this end, we have developed species-specific DNA probes for use in the rapid identification of N. fowleri from the environment. Samples were taken from the thermal springs in Bath, England, and cultured for amoebae. Of 84 isolates of thermophilic Naegleria spp., 10 were identified as N. fowleri by probe hybridization. The identity of these isolates was subsequently confirmed by their specific whole-cell DNA restriction fragment length polymorphisms (RFLPs). One DNA clone was found to contain a repeated element that detected chromosomal RFLPs that were not directly visible on agarose gels. This enabled the further differentiation of strains within geographically defined whole-cell DNA RFLP groups. N. fowleri DNA probes represent a specific and potentially rapid method for the identification of the organism soon after primary isolation from the environment.

Detection of Naegleria fowleri cysts in environmental samples by using a DNA probe

In this study we tried to detect DNA Naegleria fowleri in artificially contaminated environmental samples, with or without sediments, containing 10(4) cysts of this pathogenic amoeba. We used two assays to extract DNA from samples: first, direct DNA extraction, which gave positive results only for water samples without sediment; second, DNA extraction after sample incubation on agar plates, which allowed us to remove amoeba growing out of the sediments, and which gave positive results for all samples, even those initially with sediments (5, 500 or 500 mg). Thus, this molecular identification appears as a powerful tool to investigate N. fowleri growth in environmental samples.

Differentiation of Naegleria fowleri and other Naegleriae by polymerase chain reaction and hybridization methods

In order to detect and identify Naegleria fowleri strains an assay based on the Polymerase Chain Reaction (PCR) was evaluated. The amplified DNA fragments were detected by gel electrophoresis and ethidium bromide staining, followed by Southern blot hybridization with an internal digoxigenin-labeled probe. A set of primers (B1B2) which flank a 678-bp region within a virulence-associated gene, allowed for the highly specific identification of N. fowleri, since Naegleriae (N. lovaniensis, N. australiensis, N. gruberi, N. andersoni and N. jadini) and other Protozoa did not react. These primers did not detect amplification products from various organisms: Gram-positive bacteria, Gram-negative bacteria, algae, yeasts and human DNA. Whereas a second set of primers (A1A2), which flank a different sequence, detected various Naegleriae and Acanthamoebae strains. After 40 amplification cycles, the limit of detection was a single cell (cyst or trophozoite). Thus, the PCR appears to be a rapid and powerful tool for identification and detection of N. fowleri.

Restriction-fragment-length polymorphism and variation in electrophoretic karyotype in Naegleria fowleri from Japan

Strains of Naegleria fowleri isolated in Japan from two different places were found to differ in electrophoretic karyotype and restriction-fragment-length polymorphism (RFLP) both from each other and from strains isolated on other continents. Using the Wagner parsimony method on the RFLP, we found that the Japanese isolates are most closely related to the Australian isolates and most distinct from the European isolates.

Genotyping Naegleria spp. and Naegleria fowleri isolates by interrepeat polymerase chain reaction

All six Naegleria species recognized to date were studied by interrepeat polymerase chain reaction (PCR). Priming at repeat sequences, which are known to be variable among eukaryotes, yielded electrophoretic DNA banding patterns that were specific for any single species. With a single PCR and simple gel electrophoresis, species determination could be performed in less than 1 day. Unambiguous discrimination between the pathogen N. fowleri and nonpathogenic Naegleria species appeared to be possible. Analysis of DNAs obtained from 20 separate isolates of N. fowleri revealed that geographic variation of the genetic fingerprints rarely occurs. All but 3 of 20 isolates of N. fowleri which were investigated showed identical banding patterns; for two isolates from New Zealand and one from Australia, a limited number of additional bands was detected, independent of the PCR primers used. These data corroborate previous findings on the genetic stability of pathogenic N. fowleri.

Appearance in Europe ofNaegleria fowleri displaying the Australian type of restriction-fragment-length polymorphism

We report for the first time the isolation in Europe of Naegleria fowleri showing a type of restriction-fragment-length polymorphism (RFLP) usually found in Australia. The presence of this type as well as the European type fluctuated with time in the cooling waters of the nuclear power station investigated. Two possible explanations for the appearance of the Australian N. fowleri type in Europe are presented.

Identification of Acanthamoeba at the generic and specific levels using the polymerase chain reaction

We have adapted the polymerase chain reaction to identify strains of Acanthamoeba. Using computer-assisted analysis, primers were designed from an anonymous repetitive sequence and from published sequences of 18S and 5S ribosomal RNA genes of A. castellanii. Amplification of a short ribosomal DNA target (272 base pairs) at restrictive annealing conditions (greater than 50 degrees C) resulted in a single band that was unique for the genus and distinguished Acanthamoeba from Naegleria. This assay functioned with fresh and formalin-fixed cells as starting material. Amplification of longer targets (400-700 base pairs) at less restrictive annealing conditions (less than 47 degrees C) led to more than one band. This multiple banding pattern could reproducibly classify Acanthamoeba at the strain level and was, in certain cases, diagnostic for known pathogenic strains. However, these assays need to be further refined to make them relevant for clinical purposes.

Amplification of repetitive DNA for the specific detection of Naegleria fowleri

By using hybridization at low C0t values, a genomic library on Naegleria fowleri was screened for clones containing repetitive DNA. Partial sequence information from a repetitive clone, Nf9, showed sequence homologies with the mitochondrial ATPase 6 subunit from yeasts and other organisms. Synthetic DNA primers were selected and tested in amplification reactions. Nonstringent hybridization conditions were defined which allowed amplification of N. fowleri DNA and reduced amplification of DNA from nonpathogenic Naegleria species. Stringent conditions were selected which allowed detection only of N. fowleri. Identity of the amplified DNA was confirmed by using internal restriction sites and an internal primer. In a blind study, tissue from mice experimentally infected with N. fowleri was specifically detected by using stringent hybridization conditions.

Thermal ecology of Naegleria fowleri from a power plant cooling reservoir

The pathogenic, free-living amoeba Naegleria fowleri is the causative agent of human primary amebic meningoencephalitis. N. fowleri has been isolated from thermally elevated aquatic environments worldwide, but temperature factors associated with occurrence of the amoeba remain undefined. In this study, a newly created cooling reservoir (Clinton Lake, Illinois) was surveyed for Naegleria spp. before and after thermal additions from a nuclear power plant. Water and sediment samples were collected from heated and unheated arms of the reservoir and analyzed for the presence of thermophilic Naegleria spp. and pathogenic N. fowleri. Amoebae were identified by morphology, in vitro cultivation, temperature tolerance, mouse pathogenicity assay, and DNA restriction fragment length analysis. N. fowleri was isolated from the thermally elevated arm but not from the ambient-temperature arm of the reservoir. The probability of isolating thermophilic Naegleria and pathogenic N. fowleri increased significantly with temperature. Repetitive DNA restriction fragment profiles of the N. fowleri Clinton Lake isolates and a known N. fowleri strain of human origin were homogeneous.

Evaluation of evolutionary divergence in the genus Naegleria by analysis of ribosomal DNA plasmid restriction patterns

Ribosomal DNA (rDNA) plasmid restriction maps of 10 strains and rDNA hybridisation patterns of 61 additional strains have been used to assess inter- and intra-specific diversity and phylogenetic relationships in the genus Naegleria. The results obtained by this method largely confirm those of previous studies based on a variety of other criteria. They indicate that very little variation exists within the pathogenic species Naegleria fowleri despite its worldwide distribution and that it is closely related to the nonpathogenic Naegleria lovaniensis. Naegleria gruberi is most likely a polyphyletic grouping and care should be taken when using one strain as a reference point for this species. In addition, the two subspecies of the pathogenic Naegleria australiensis arose separately from within the range of variability encompassed by N. gruberi, as did the species Adelphamoeba galeacystis which should probably be assigned to the genus Naegleria. The species Naegleria jadini and Naegleria andersoni are not closely related to any other in the genus based on their rDNA patterns.

Variation of electrophoretic karyotypes among Naegleria spp

All species and subspecies of the genus Naegleria were subjected to karyotype analysis by contour-clamped homogeneous electric field and transverse alternating-field electrophoresis. The former technique proved to be superior in detecting differences in karyotype. The chromosome pattern of each species and subspecies was found to be distinct. Between 15 and 23 bands were resolved, with chromosome sizes ranging from a few hundred kilobases to about 1.5 Mb. Hybridisation with cloned rDNA identified one band in all species, corresponding to the rDNA plasmid that does not migrate according to its molecular weight because it is circular. In Willaertia magna a similar size distribution was found, in contrast to Giardia and Entamoeba, which have only very large chromosomes. Within the pathogenic N. fowleri some strains showed slight differences in chromosome pattern. The karyotype differed more between strains within the subspecies N. and andersoni than between the two species N. fowleri and N. lovaniensis. The results suggest that karyotype analysis cannot be used to identify a Naegleria species but is useful for stock identification, gene localisation, genetic exchange studies and epidemiological investigation of the pathogenic N. fowleri.