The parasite that causes whirling disease, Myxobolus cerebralis, is genetically variable within and across spatial scales

Understanding the genetic structure of parasite populations on the natural landscape can reveal important aspects of disease ecology and epidemiology and can indicate parasite dispersal across the landscape. Myxobolus cerebralis (Myxozoa: Myxosporea), the causative agent of whirling disease in the definitive host Tubifex tubifex, is native to Eurasia and has spread to more than 25 states in the USA. The small amounts of data available to date suggest that M. cerebralis has little genetic variability. We examined the genetic variability of parasites infecting the definitive host T. tubifex in the Madison River, MT, and also from other parts of North America and Europe. We cloned and sequenced 18S ribosomal DNA and the internal transcribed spacer-1 (ITS-1) gene. Five oligochaetes were examined for 18S and five for ITS-1, only one individual was examined for both genes. We found two different 18S rRNA haplotypes of M. cerebralis from five worms and both intra- and interworm genetic variation for ITS-1, which showed 16 different haplotypes from among 20 clones. Comparison of our sequences with those from other studies revealed M. cerebralis from MT was similar to the parasite collected from Alaska, Oregon, California, and Virginia in the USA and from Munich, Germany, based on 18S, whereas parasite sequences from West Virginia were very different. Combined with the high haplotype diversity of ITS-1 and uniqueness of ITS-1 haplotypes, our results show that M. cerebralis is more variable than previously thought and raises the possibility of multiple introductions of the parasite into North America.     

Myxobolus cerebralis internal transcribed spacer 1 (ITS-1) sequences support recent spread of the parasite to North America and within Europe

Molecular approaches for resolving relationships among the Myxozoa have relied mainly on small subunit (SSU) ribosomal DNA (rDNA) sequence analysis. This region of the gene is generally used for higher phylogenetic studies, and the conservative nature of this gene may make it inadequate for intraspecific comparisons. Previous intraspecific studies of Myxobolus cerebralis based on molecular analyses reported that the sequence of SSU rDNA and the internal transcribed spacer (ITS) were highly conserved in representatives of the parasite from North America and Europe. Considering that the ITS is usually a more variable region than the SSU, we reanalyzed available sequences on GenBank and obtained sequences from other M. cerebralis representatives from the states of California and West Virginia in the USA and from Germany and Russia. With the exception of 7 base pairs, most of the sequence designated as ITS-1 in GenBank was a highly conserved portion of the rDNA near the 3-prime end of the SSU region. Nonetheless, the additional ITS-1 sequences obtained from the available geographic representatives were well conserved. It is unlikely that we would have observed virtually identical ITS-1 sequences between European and American M. cerebralis samples had it spread naturally over time, particularly when compared to the variation seen between isolates of another myxozoan (Kudoa thyrsites) that has most likely spread naturally. These data further support the hypothesis that the current distribution of M. cerebralis in North America is a result of recent introductions followed by dispersal via anthropogenic means, largely through the stocking of infected trout for sport fishing.     

Comparison of small subunit ribosomal RNA gene and internal transcribed spacer sequences among isolates of the intranuclear microsporidian Nucleospora salmonis

Nucleospora salmonis is an intranuclear microsporidian associated with a proliferative disorder of the lymphoid cells of captive salmonid fish in the northwestern and northeastern regions of North America, in France, and in Chile. Newer diagnostic approaches have used the polymerase chain reaction (PCR) to detect the parasite in fish tissues. The target sequences for these assays lie in the small subunit ribosomal RNA (ssu rRNA) gene or internal transcribed spacer (ITS) as determined from N. salmonis from chinook salmon (Oncorhynchus tshawytscha) from the Pacific Northwest of North America. The lack of sequence data on parasites from diverse geographic origins and hosts led us to compare several isolates of N. salmonis. There was a high degree of similarity in the ssu rDNA sequences (> 98%) among all the isolates of N. salmonis examined, regardless of host or geographic origin. The greatest sequence differences were found between isolates from the Pacific regions of America. Isolates from Chile shared sequences with one or both geographic groups from North America. A similar distribution of sequence types was observed when ITS-1 sequences of selected isolates were analyzed. Sequence data from two N. salmonis-like isolates from marine non-salmonid fish showed one closely related and the second less closely related to N. salmonis isolates from salmonid fish. These results provide evidence for a homogeneous group of aquatic members of the genus Nucleospora found among salmonid fish (N. salmonis) that can be detected using diagnostic PCR assays with ssu rDNA target sequences. The presence of parasites related to N. salmonis among marine fish suggests a potentially broad host and geographic distribution of members of the family Enterocytozoonidae.     

Comparison of the internal transcribed spacer, ITS-1, from Sarcocystis falcatula isolates and Sarcocystis neurona.

The genetic diversity among 6 Sarcocystis falcatula isolates derived from geographically distinct regions in the U.S.A. was detected using the first internal transcribed spacer region 1 (ITS-1) of the rRNA gene. These sequences were then compared to the full sequence from a Sarcocystis neurona isolate obtained from a California horse diagnosed with equine protozoal myeloencephalitis. No nucleotide differences were detected over partial sequence analysis of 2 additional S. neurona isolates: however, the complete nucleotide sequence for the ITS-1 region was not compared. Twelve nucleotide differences were consistently detected when aligned sequences of S. neurona were compared to those of the S. falcatula isolates. Additional nucleotide base changes were detected among the S. falcatula isolates, but these changes were not consistent in all the S. falcatula isolates. These results indicate that S. falcatula may be comprised of a heterogeneous population and that the ITS-1 region can be used to distinguish S. neurona from S. falcatala used in this study.     

Intraspecific Variation in Cryptocaryon irritans

ABSTRACT. Intraspecific variation in the ciliate Cryptocaryon irritans was examined using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA) combined with developmental and morphological characters. Amplified rDNA sequences consisting of 151 bases of the flanking 18 S and 5.8 S regions, and the entire ITS-1 region (169 or 170 bases), were determined and compared for 16 isolates of C. irritans from Australia, Israela and the USA. There was one variable base between isolates in the 18 S region nd 11 variables indicate that Australian C. irritans isolates from estuarine (Moreton Bay) and coral reef (Heron Island) environments are distinct. The Heron Island isolate was genetically closer to morphologically dissimilar isolates from Israel (1.8% divergence) and USA (2.3 % divergence) than it was to the Moreton Bay isolates. Three isolates maintained in our laboratory since February 1994 originated from the same source. During this time the sequence of the isolates from wild fish in Moreton Bay remained unchanged. These genetic differences indicate the existence of a founder effects in laboratorty populations of C. irritans . The genetic variation found here, combined with known morphological and developmental differences, is used to characterise four strains of C. irritans .     

Molecular characterization of Fasciola hepatica from Sardinia based on sequence analysis of genomic and mitochondrial gene markers

The aim of the present study is to investigate for the first time the genetic diversity of samples identified morphologically as Fasciola hepatica (Platyhelminthes: Trematoda: Digenea) (n = 66) from sheep and cattle from two localities of Sardinia and to compare them with available data from other localities by partial sequences of the first (ITS-1), the 5.8S, and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA) genes, the mitochondrial cytochrome c oxidase subunit I (COI), and nicotinamide adenine dinucleotide dehydrogenase subunit I (ND1) genes. Comparison of the sequences from Sardinia with sequences of Fasciola spp. from GenBank confirmed that all samples belong to the species F. hepatica. The nucleotide sequencing of ITS rDNA showed no nucleotide variation in the ITS-1, 5.8S and ITS-2 rDNA sequences among all Sardinian samples, comparing with two ITS-2 haplotypes in standard F. hepatica, showing a substitution C/T in 20 position 859, reported previously from Tunisia, Algeria, Australia, Uruguay and Spain. The present study shows that in Sardinian sheep and cattle there is the most frequent haplotype (FhITS-H1) of F. hepatica species from South Europe. Considering NDI sequences, the phylogenetic trees showed reliable grouping among the haplotypes of F. hepatica from Sardinia and the mitochondrial lineage I, including the main N1 haplotype, observed previously from Europe (Russia, Belarus, Ukraine and Bulgaria), Armenia, West Africa (Nigeria), America (Uruguay and USA), Asia (Turkey, Japan, and China), Georgia, Turkmenistan, Azerbaijan and Australia. Furthermore, common haplotypes FhCOI-H1 and FhCOI-H2 of F. hepatica from Sardinia also corresponded mostly to the first lineage including the main C1 haplotype reported previously from Eastern European and Western Asian populations, they belonged just to a phylogenically distinguishable clade, as F. hepatica from Australia, France, Turkey, Uruguay, Russia, Armenia, Ukraine, Belarus, Turkmenistan, USA, Tunisia and Algeria, indicating that this is the main haplotype involved in the spread of F. hepatica throughout all continents.     

Nucleotide diversity of Japanese isolates of infectious hematopoietic necrosis virus (IHNV) based on the glycoprotein gene

Infectious hematopoietic necrosis virus (IHNV), a member of the genus Novirhabdovirus, causes a highly lethal disease of salmonid fish. In the present study, G gene nucleotide sequences of 9 Japanese IHNV isolates obtained from 1971 to 1996 were analyzed to evaluate the genetic diversity and compared with IHNV isolates from North America and Europe. A radial phylogenetic tree revealed 5 major clusters including 3 genogroups (U, M and L) for North American isolates and 1 genogroup for European isolates. Five Japanese isolates from 1971 to 1982 appeared in the cluster for genogroup U, while the remaining Japanese isolates from 1980 to 1996 formed a new genogroup, JRt (Japanese rainbow trout). Maximum nucleotide diversity among the Japanese isolates was 4.5%, which was greater than that within the North American isolates (3.6%), and the degree of nucleotide diversity within Japanese isolates was increased by inclusion of the genogroup JRt isolates. It was concluded that Japanese isolates shared a common source with the genogroup U of the North American isolates and that there were large divergences between Japanese isolates before and after the 1980s.     

Disparate infection patterns of Ceratomyxa shasta (Myxozoa) in rainbow trout (Oncorhynchus mykiss) and Chinook salmon (Oncorhynchus tshawytscha) correlate with internal transcribed spacer-1 sequence variation in the parasite

Ceratomyxa shasta is a virulent myxosporean parasite of salmon and trout in the Pacific Northwest of North America. The parasite is endemic in the Klamath River, Oregon/California, where a series of dams prevent movement of fish hosts between the upper and lower parts of the basin. Ceratomyxa shasta exhibits a range of infection patterns in different fish species above and below the dams. We hypothesised that the variations in infection and disease are indicators that different strains of the parasite exist, each with distinct host associations. Accordingly, we sought to identify strain-specific genetic markers in the ssrRNA and internal transcribed spacer region 1 (ITS-1). We examined 46 C. shasta isolates from water samples and two fish hosts, from June 2007 field exposures at upper and lower Klamath River sites with similarly high parasite densities. We found 100% of non-native rainbow trout became infected and died at both locations. In contrast, mortality in native Chinook salmon was <10% in the upper basin, compared with up to 40% in the lower basin. Parasite ssrRNA sequences were identical from all fish. However, ITS-1 sequences contained multiple polymorphic loci and a trinucleotide repeat (ATC)_0-3 from which we defined four genotypes: 0, I, II and III. Non-native rainbow trout at both sites were infected with genotype II and with a low level of genotype III. Chinook salmon in the upper basin had genotypes II and III, whereas in the lower basin genotype I predominated. Genotype I was not detected in water from the upper basin, a finding consistent with the lack of anadromous Chinook salmon there. Genotype O was only detected in water from the upper basin. Resolution of C. shasta into sympatric, host-specific genotypes has implications for taxonomy, monitoring and management of this significant parasite.     

Presence of methicillin-resistant Staphylococcus aureus in pigs in Peru

We report the first detection of methicillin-resistant Staphylococcus aureus isolates in pigs in Peru. The isolates belong to a livestock-associated lineage previously reported in North America and Europe, CC398, and a highly virulent USA300-like ST8-IV variant, which is the predominant community-associated lineage in Latin America.     

The phylogeography of salmonid proliferative kidney disease in Europe and North America

Salmonid proliferative kidney disease (PKD) is caused by the myxozoan Tetracapsuloides bryosalmonae. Given the serious and apparently growing impact of PKD on farmed and wild salmonids, we undertook a phylogeographic study to gain insights into the history of genealogical lineages of T. bryosalmonae in Europe and North America, and to determine if the global expansion of rainbow trout farming has spread the disease. Phylogenetic analyses of internal transcribed spacer 1 sequences revealed a clade composed of all North American sequences plus a subset of Italian and French sequences. High genetic diversity in North America and the absence of genotypes diagnostic of the North American clade in the rest of Europe imply that southern Europe was colonized by immigration from North America; however, sequence divergence suggests that this colonization substantially pre-dated fisheries activities. Furthermore, the lack of southern European lineages in the rest of Europe, despite widespread rainbow trout farming, indicates that T. bryosalmonae is not transported through fisheries activities. This result strikingly contrasts with the commonness of fisheries-related introductions of other pathogens and parasites and indicates that fishes may be dead-end hosts. Our results also demonstrate that European strains of T. bryosalmonae infect and induce PKD in rainbow trout introduced to Europe.     

Characterisation of a low pathogenic form of Gyrodactylus salaris from rainbow trout

Gyrodactylus salaris was isolated from rainbow trout in a Danish freshwater trout farm, and a laboratory population of this particular parasite form was established on rainbow trout. Challenge infections were performed using different salmonid strains and species, including East Atlantic salmon Salmo salar (from the Danish River Skjern?), Baltic salmon S. salar (from the Swedish River Ume Alv) and rainbow trout Oncorhynchus mykiss (from the Danish rainbow trout farm Fousing). These were compared to infection studies on the Norwegian Laerdalselva parasite form kept under exactly the same conditions in the laboratory. The Danish G. salaris form had low virulence towards both Atlantic and Baltic salmon, whereas rainbow trout proved susceptible to the parasite. The Danish G. salaris form was able to maintain a very low infection on East Atlantic salmon, but not on the Baltic salmon, which eliminated the infection within 2 wk. Rainbow trout developed infection intensities ranging up to several hundred parasites per host. The host colonization patterns of the parasite differed clearly from those of previous studies on microhabitats of the Norwegian form of G. salaris. A comparative study on morphological characters (opisthaptoral hard parts) from the Danish parasite form and Norwegian G. salaris showed no significant differences. Selected genes comprising internal transcribed spacers 1 and 2 (ITS), ribosomal RNA intergenic spacer (IGS) and cytochrome c oxidase subunit I (COI) regions were cloned and sequenced. Five sequenced ITS clones from 5 individuals of the Danish strain consistently revealed a single base substitution compared to ITS sequences from all other known species and strains of Gyrodactylus. Mitochondrial COI gene sequences demonstrated that the Danish G. salaris form is closely similar to the Laerdalselva parasite form found in Norway. The IGS sequences were highly variable, but very similar to those obtained from German isolates of G. salaris.     

Molecular and pathobiological characterization of 61 Potato mop‐top virus full‐length cDNAs reveals great variability of the virus in the centre of potato domestication,novel genotypes and evidence for recombination

The evolutionary divergence of Potato mop‐top virus (PMTV), a tri‐partite, single‐stranded RNA virus, is exceptionally low, based on the analysis of sequences obtained from isolates from Europe, Asia and North America. In general, RNA viruses exist as dynamic populations of closely related and recombinant genomes that are subjected to continuous genetic variation. The reason behind the low genetic variation of PMTV remains unclear. The question remains as to whether the low variability is a shared property of all PMTV isolates or is a result of the limited number of isolates characterized so far. We hypothesized that higher divergence of the virus might exist in the Andean regions of South America, the centre of potato domestication. Here, we report high variability of PMTV isolates collected from 12 fields in three locations in the Andean region of Peru. To evaluate PMTV genetic variation in Peru, we generated full‐length cDNA clones, which allowed reliable comparative molecular and pathobiological characterization of individual isolates. We found significant divergence of the CP‐RT and 8K sequences. The 8K cistron, which encodes a viral suppressor of RNA silencing, was found to be under diversifying selection. Phylogenetic analysis determined that, based on the CP‐RT sequence, all PMTV isolates could be categorized into three separate lineages (clades). Moreover, we found evidence for recombination between two clades. Using infectious cDNA clones of the representatives of these two clades, as well as reassortants for the RNA‐CP genomic component, we determined the pathobiological differences between the lineages, which we coined as S (for severe) and M (for mild) types. Interestingly, all isolates characterized previously (from Europe, Asia and North America) fall into the S‐type clade, whereas most of the Peruvian isolates belong to the M‐type. Taken together, our results support the notion of the single introduction of PMTV from the centre of potato origin to Europe, and subsequent spread of the S‐type into Asia and USA. This is also supported by the suggested novel classification of isolates based on genetic constellations.     

Morphological and molecular characterisation of Puccinia lagenophorae, now present in central North America

In June 2004, a rust fungus not previously reported for Oklahoma was found occurring naturally on the weed, common groundsel, Senecio vulgaris, in pots in a commercial container nursery in northeastern Oklahoma. Host symptoms and morphology of teliospores and aeciospores of the fungus were consistent with those of Puccinia lagenophorae, a recent introduction into North America that has, as yet, been reported only on the East and West Coasts of the USA. This is the first report of the rust in central regions of North America. The rust is believed to be native to Australia and New Zealand and subsequently reported in most continents on numerous species and genera of the Asteraceae. Some authors in Europe consider the rust on Bellis as different from the one on Senecio, naming it Puccinia distincta. Our ITS1‐5.8S‐ITS2 ribosomal DNA sequence data, however, show homology with P. distincta sequences from Europe, indicating there is only one morphologically‐variable polyphagous species. Presumably, the rust was introduced into Oklahoma on infected plants from the West Coast of the USA, the source of most plant material in the commercial nursery where it was found. The rust is potentially important on several ornamental Asteraceae in North America as it has become in Europe, where it spreads rapidly throughout that continent following its introduction there in the early 1960s.     

Observations on the diversity and ecology of freshwater Nannochloropsis (Eustigmatophyceae), with descriptions of new taxa

The genus Nannochloropsis is well known from the marine environment but has only recently been reported from fresh and brackish waters. A single species, N. limnetica, was first documented from shallow lakes in Germany, where it produced spring blooms. A second unnamed isolate from a river in the United States has been characterized by sequence analysis and light microscopy. All of the Nannochloropsis species that have been described, both marine and freshwater, are small spheres with essentially no distinguishing morphological characteristics. Therefore, they must be characterized using molecular techniques. We have cultured numerous isolates of Nannochloropsis from a series of lakes on the James River in the Arrowwood National Wildlife Refuge, North Dakota, USA, and 1 isolate from a pond in Itasca State Park, Minnesota, USA. The diversity among these isolates was determined by light microscopy and DNA sequence analysis. Seven distinct haplotypes of Nannochloropsis were found, one of which possesses 18S rDNA and rbcL sequences identical to those of N. limnetica from Europe. The 6 new haplotypes vary in rbcL sequences and some are morophologically distinct from each other and from N. limnetica. These types are described as the new taxa N. limnetica var. globosa, N. limnetica var. irregularis, N. limnetica var. dystrophica, and N. limnetica var. gutta. All of the Nannochloropsis isolates from Arrowwood and Itasca were cultured only from samples taken during cold-water periods. These results suggest that Nannochloropsis species may be better adapted to cold water conditions, including temperatures near 0 degrees C and ice cover.     

Rapid global spread of two aggressive strains of a wheat rust fungus

Rust fungi can overcome the effect of host resistance genes rapidly, and spores can disperse long distance by wind. Here we demonstrate a foreign incursion of similar strains of the wheat yellow rust fungus, Puccinia striiformis f. sp. tritici , in North America, Australia and Europe in less than 3 years. One strain defined by identity at 15 virulence loci and 130 amplified fragment length polymorphism (AFLP) fragments was exclusive to North America (present since 2000) and Australia (since 2002). Another strain of the same virulence phenotype, but differing in two AFLP fragments, was exclusive to Europe (present since 2000–2001) as well as Western and Central Asia and the Red Sea Area (first appearance unknown). This may be the most rapid spread of an important crop pathogen on the global scale. The limited divergence between the two strains and their derivatives, and the temporal–spatial occurrence pattern confirmed a recent spread. The data gave evidence for additional intercontinental dispersal events in the past, that is, many isolates sampled before 2000 in Europe, North America and Australia had similar AFLP fingerprints, and isolates from South Africa, which showed no divergence in AFLP, differed by only two fragments from particular isolates from Central Asia, West Asia and South Europe, respectively. Previous research has demonstrated that isolates of the two new strains produced up to two to three times more spores per day than strains found in USA and Europe before 2000, suggesting that increased aggressiveness at this level may accelerate global spread of crop pathogens.     

Analysis of Intraspecific Sequence Variation Among Eight Isolates of the Rumen Symbiont, Isotricha prostoma (Ciliophora), from Two Continents

The internally transcribed spacer regions 1 and 2 (ITS-1 and ITS-2) and the 5.8S ribosomal RNA gene of Isotricha prostoma were examined for intraspecific sequence variation. There were no differences in the ITS-1/5.8S/ITS-2 region among cattle and sheep isolates of I. prostoma from Australia, Canada, and the United States, indicating that this region is 100% conserved among eight isolates from two continents.     

Molecular identification of Babesia parasites isolated from Ixodes ricinus ticks collected in northwestern Poland

In the present study, PCR has been applied to detect and analyze DNA of Babesia spp. extracted from Ixodes ricinus ticks. Collection of I. ricinus was made in 6 forested areas of Zachodniopomorskie Voivodship, Poland, during 2 seasonal peaks of tick activity, i.e., spring and autumn, 2001. In total, 1,328 I. ricinus were collected and processed for PCR with F34 and R323 primers. Babesia spp. was detected in 28 (2% of 1,328 tested) ticks; 26 were identified as B. divergens. The other 2 were identified as B. microti. PCR was conducted with 18S rRNA specific primers and sequencing was processed to precisely identify and compare these isolates with B. microti and B. divergens sequences from Europe, North America, and Asia obtained from the GenBank. Analysis revealed that sequences of B. microti from northwestern Poland are almost identical (99.94%) with those referred to as "Munich strain"; both form a clade different from other European strains, as well as those from Asia and North America (called B. microti, sensu stricto). An investigation performed with B. divergens sequences showed that the sequence from northwestern Poland is 99.94% homologous to an isolate from Ireland ("Purnel"), and differs in just a few nucleotides from other European sequences. Phylogenetic analysis revealed that the sequence of B divergens isolated from Polish ticks form a group that comprise 4 European sequences from Great Britain and Ireland and is, therefore, closely related to other European and North American B. divergnens sequences.     

Molecular characterization of hard tick <Emphasis Type="Italic">Haemaphysalis longicornis</Emphasis> from China by sequences of the internal transcribed spacers of ribosomal DNA

In the present study, the entire first and second internal transcribed spacer (ITS-1 and ITS-2) regions of nuclear ribosomal DNA (rDNA) of Haemaphysalis longicornis from China were amplified by polymerase chain reaction. The 45 representative amplicons were sequenced, and sequence variation in the ITS was examined. The ITS sequences of H. longicornis were 3644 bp in size, including the part of 18S rDNA, 28S rDNA sequences and the complete ITS-1, 5.8S rDNA and ITS-2 sequences. Sequence analysis revealed that the ITS-1, 5.8S rDNA and ITS-2 of this hard tick were 1582, 152, and 1610 bp in size, respectively. The intra-specific sequence variations of ITS-1 and ITS-2 within H. longicornis were 0–2 and 0–2.2%; however, the inter-specific sequence differences among members of the genus Haemaphysalis were significantly higher, being 35.1–55.2 and 37–52% for ITS-1 and ITS-2, respectively. The molecular approach employed in this study provides the foundation for further studies of the genetic variation of H. longicornis from different hosts and geographical origins in China.     

Characterization of Cryptocaryon irritans,a parasite isolated from marine fishes in Taiwan

The ciliated protozoan parasite Cryptocaryon irritans infecting marine fishes in Taiwan is described. Developmental characteristics and sequences of the ribosomal DNA regions such as part of 18 S, the entire first internal transcribed spacer, and part of 5.8 S of various Taiwan isolates of C. irritans were investigated. A total of 5 isolates was obtained from different fish-host species and localities, the majority from cultured fish species. C. irritans from Taiwan is able to shift its developmental characteristics, i.e. from non-adherent to adherent tomonts, from individualistic to aggregate-forming tomonts, from infection of the gills only to infection of the gills and body. Thus, it is not possible to classify strains of C. irritans on the basis of these parameters. Premature tomonts that developed from dead fishes were able to produce theronts that could infect fish host. Isolates from Pingtung and the USA had identical nucleotide sequences while an isolate from Malaysia was identical to an Israel isolate. Percentage variation among pairs of Taiwan isolates showed a higher degree of variation than isolate sequences listed in GenBank. Sequence analysis revealed highly aberrant isolates in Taiwan, and a phylogenetic tree distinguished a marine and a low-salinity variant. C. irritans from marine fishes in Taiwan, therefore, display some characteristics not previously reported. Since manipulation of salinity in brackishwater ponds and marine cage sites is not feasible, there is a need to develop new strategies for the control and prevention of cryptocaryoniasis.