scholarly journals Occurrence ofTerranovalarval types (Nematoda: Anisakidae) in Australian marine fish with comments on their specific identities

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1722 ◽  
Author(s):  
Shokoofeh Shamsi ◽  
Jaydipbhai Suthar
Keyword(s):  
Marine Fish ◽  
Sequence Data ◽  
Infected Fish ◽  
Human Infection ◽  
Internal Transcribed Spacers ◽  
Accurate Identification ◽  
Essential Information ◽  
Larval Type ◽  
Morphological Criteria ◽  
Specific Identity

Pseudoterranovosis is a well-known human disease caused by anisakid larvae belonging to the genusPseudoterranova. Human infection occurs after consuming infected fish. Hence the presence ofPseudoterranovalarvae in the flesh of the fish can cause serious losses and problems for the seafood, fishing and fisheries industries. The accurate identification ofPseudoterranovalarvae in fish is important, but challenging because the larval stages of a number of different genera, includingPseudoterranova,TerranovaandPulchrascaris, look similar and cannot be differentiated from each other using morphological criteria, hence they are all referred to asTerranovalarval type. Given thatTerranovalarval types in seafood are not necessarilyPseudoterranovaand may not be dangerous, the aim of the present study was to investigate the occurrence ofTerranovalarval types in Australian marine fish and to determine their specific identity. A total of 137 fish belonging to 45 species were examined.Terranovalarval types were found in 13 species, some of which were popular edible fish in Australia. The sequences of the first and second internal transcribed spacers (ITS-1 and ITS-2 respectively) of theTerranovalarvae in the present study showed a high degree of similarity suggesting that they all belong to the same species. Due to the lack of a comparable sequence data of a well identified adult in the GenBank database the specific identity ofTerranovalarval type in the present study remains unknown. The sequence of the ITS regions of theTerranovalarval type in the present study and those ofPseudoterranovaspp. available in GenBank are significantly different, suggesting that larvae found in the present study do not belong to the genusPseudoterranova, which is zoonotic. This study does not rule out the presence ofPseudoterranovalarvae in Australian fish asPseudoterranova decipiens Ehas been reported in adult form from seals in Antarctica and it is known that they have seasonal presence in Australian southern coasts. The genetic distinction ofTerranovalarval type in the present study fromPseudoterranovaspp. along with the presence of more species of elasmobranchs in Australian waters (definitive hosts ofTerranovaspp. andPulchrascarisspp.) than seals (definitive hosts ofPseudoterranovaspp.) suggest thatTerranovalarval type in the present study belong to either genusTerranovaorPulchrascaris, which are not known to cause disease in humans. The present study provides essential information that could be helpful to identify AustralianTerranovalarval types in future studies. Examination and characterisation of further specimens, especially adults ofTerranovaandPulchrascaris, is necessary to fully elucidate the identity of these larvae.

Morphometric and molecular descriptions of three new species of Hysterothylacium (Nematoda: Raphidascarididae) from Australian marine fish

2016 ◽  
Vol 91 (5) ◽  
pp. 613-624 ◽  
Author(s):  
S. Shamsi
Keyword(s):  
New Species ◽  
Marine Fish ◽  
Sequence Data ◽  
Internal Transcribed Spacers ◽  
Its Sequences ◽  
Larval Type ◽  
Third Stage ◽  
Three New Species ◽  
Paratenic Hosts ◽  
Seriola Lalandi

AbstractThree new species of Hysterothylacium Ward & Magath, 1917, including H. australe, H. kajikiae and H. brucei, from Australian marine fish are described and illustrated by light microscopy followed by genetic characterization of their first and second internal transcribed spacers (ITS-1 and ITS-2, respectively). This is the first study reporting ITS sequence data for adult Hysterothylacium spp. in Australia, which provides an insight into the identification of some of the Hysterothylacium larval types. Alignment of ITS sequences of these species with Hysterothylacium larval types previously reported in Australia showed that fourth-stage Hysterothylacium larval type XI from Seriola lalandi and third-stage Hysterothylacium larval type X from Sphyraene novae-hollandiae are identical with ITS sequences of H. australe, suggesting that these fish are natural intermediate/paratenic hosts of H. australe.

scholarly journals Ultramorphology and molecular studies of Contracaecum larvae (Nematoda: Anisakidae) collected in five Cyprinid fish species from Sulaimani Province, Kurdistan Region-Iraq

2021 ◽  
Vol 58 (1) ◽  
pp. 41-58
Author(s):  
Y. S. Abdullah ◽  
S. M. A. Abdullah ◽  
R. H. Hussein
Keyword(s):  
Molecular Analysis ◽  
Fish Species ◽  
Infected Fish ◽  
Internal Transcribed Spacers ◽  
Kurdistan Region ◽  
Accurate Identification ◽  
Contracaecum Rudolphii ◽  
C Subunit ◽  
Polymerase Chain ◽  
Cox 2

Summary A total of 1134 freshwater fishes belonging to Cyprinidae (Acanthobrama marmid (n=20), Alburnus caeruleus (n=7), Alburnus mossulensis (n=62), Arabibarbus grypus (n=123), Barbus lacerta (n=7), Capoeta trutta (n=222), C. umbla (n=161), Carasobarbus kosswigi (n=5), C. luteus (n=89), Carassius auratus (n=54), Chondrostoma regium (n=52), Cyprinion kais (n=10) and C. macrostomum (n=322)) were collected in different water bodies in Sulaimani Province, Kurdistan Region-Iraq for the presence of larval nematode of the genus Conteacaecum. This investigation revealed that 17 fishes belonged to five species (A. marmid, A. grypus, C. trutta, C. luteus and C. regium) were infected with Contracaecum larvae with prevalence of 35 %, 0.81 %, 0.90 %, 4.49 % and 5.76 %, respectively. The third- larval stage was morphologically studied by optical microscopy, and the ultrastructure was investigated using scanning electron microscopy (SEM). In addition, molecular analysis was carried out by amplifying, sequencing and comparing different gene loci, including internal transcribed spacers (ITS-1 and ITS-2) and cytochrome oxidase c subunit-II (COX-2), of the different isolated Contracaecum larvae. These sequences were also compared with closely related nematode sequences from the GenBank. Fifteen sequences were obtained for this study from the collected Contracaecum larvae. ITS-1, ITS-2 and COX-2 were amplified by polymerase chain reaction (PCR) and sequenced. The sequences of ITS-1, ITS-2 and COX-2 revealed that the collected Contracaecum larval specimens from all infected fish species represented one species (Contracaecum rudolphii B) based on the identity percentage in the GenBank database. The genetic characterisation of the parasite in the present study is available in the GenBank database, and the obtained ITS-1, ITS-2 and COX-2 sequences were deposited in GenBank. The present study provides information on the accurate identification and molecular analysis of Contracaecum larvae in the infected fish species in Sulaimani Province, Kurdistan Region-Iraq.

Morphological and molecular characterization of selected species of Hysterothylacium (Nematoda: Raphidascarididae) from marine fish in Iraqi waters

2017 ◽  
Vol 92 (1) ◽  
pp. 116-124 ◽  
Author(s):  
M. Ghadam ◽  
M. Banaii ◽  
E.T. Mohammed ◽  
J. Suthar ◽  
S. Shamsi
Keyword(s):  
Sequence Data ◽  
Internal Transcribed Spacers ◽  
Molecular Evidence ◽  
Fourth Stage ◽  
Larval Stages ◽  
Larval Type ◽  
Stage Of Development ◽  
Close Proximity ◽  
New Hosts ◽  
Bandar Abbas

AbstractHysterothylacium species are perhaps the most abundant and diverse group of marine ascaridoids; however, their life cycle and specific identification in larval stages in many parts of the world, particularly in Iraqi marine waters, have not been completely understood. In this study three members of the genus Hysterothylacium collected from Khor Abdulla in Iraq are morphologically described, genetically characterized and their relationship with other closely related taxa are compared and discussed. A new Hysterothylacium larval type in the fourth stage of development is described, and morphological and molecular evidence (based on the sequences of internal transcribed spacers) are provided for its distinction from previously known fourth-stage Hysterothylacium larval types. Based on the sequence data it is suggested that the new larval type, which herein was assigned as Hysterothylacium larval type XVI, is H. persicum which was previously reported from the close proximity in Bandar Abbas, Iran. In addition, two other taxa, including Hysterothylacium larval type XV and H. reliquens, have been found in the present study, for which new hosts are reported. This study provides some insights into the taxonomy and systematics of these parasites, not only in this region but also for similar studies elsewhere.

scholarly journals The Evolution of Life Modes in Stictidaceae, with Three Novel Taxa

2021 ◽  
Vol 7 (2) ◽  
pp. 105
Author(s):  
Vinodhini Thiyagaraja ◽  
Robert Lücking ◽  
Damien Ertz ◽  
Samantha C. Karunarathna ◽  
Dhanushka N. Wanasinghe ◽  
...  
Keyword(s):  
New Species ◽  
Large Scale ◽  
Sequence Data ◽  
Large Subunit ◽  
Monte Carlo Sampling ◽  
Small Subunit ◽  
Sensu Stricto ◽  
Internal Transcribed Spacers ◽  
Character State ◽  
Phenotypic Data

Ostropales sensu lato is a large group comprising both lichenized and non-lichenized fungi, with several lineages expressing optional lichenization where individuals of the same fungal species exhibit either saprotrophic or lichenized lifestyles depending on the substrate (bark or wood). Greatly variable phenotypic characteristics and large-scale phylogenies have led to frequent changes in the taxonomic circumscription of this order. Ostropales sensu lato is currently split into Graphidales, Gyalectales, Odontotrematales, Ostropales sensu stricto, and Thelenellales. Ostropales sensu stricto is now confined to the family Stictidaceae, which includes a large number of species that are poorly known, since they usually have small fruiting bodies that are rarely collected, and thus, their taxonomy remains partly unresolved. Here, we introduce a new genus Ostropomyces to accommodate a novel lineage related to Ostropa, which is composed of two new species, as well as a new species of Sphaeropezia, S. shangrilaensis. Maximum likelihood and Bayesian inference analyses of mitochondrial small subunit spacers (mtSSU), large subunit nuclear rDNA (LSU), and internal transcribed spacers (ITS) sequence data, together with phenotypic data documented by detailed morphological and anatomical analyses, support the taxonomic affinity of the new taxa in Stictidaceae. Ancestral character state analysis did not resolve the ancestral nutritional status of Stictidaceae with confidence using Bayes traits, but a saprotrophic ancestor was indicated as most likely in a Bayesian binary Markov Chain Monte Carlo sampling (MCMC) approach. Frequent switching in nutritional modes between lineages suggests that lifestyle transition played an important role in the evolution of this family.

scholarly journals Performance of Five Commercial Identification Platforms for Identification of Staphylococcus delphini

2019 ◽  
Vol 57 (11) ◽  
Author(s):  
Matthew C. Canver ◽  
Tsigereda Tekle ◽  
Samantha T. Compton ◽  
Katrina Callan ◽  
Eileen M. Burd ◽  
...  
Keyword(s):  
Distinct Species ◽  
Human Infection ◽  
Species Level ◽  
Accurate Identification ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Staphylococcus Intermedius ◽  
Animal Pathogens ◽  
Tof Ms

ABSTRACT The Staphylococcus intermedius group (SIG) is a collection of coagulase-positive staphylococci consisting of four distinct species, namely, Staphylococcus cornubiensis, Staphylococcus delphini, Staphylococcus intermedius, and Staphylococcus pseudintermedius. SIG members are animal pathogens and rare causes of human infection. Accurate identification of S. pseudintermedius has important implications for interpretation of antimicrobial susceptibility testing data and may be important for other members of the group. Therefore, we sought to evaluate the performance of five commercially available identification platforms with 21 S. delphini isolates obtained from a variety of animal and geographic sources. Here, we show that automated biochemical platforms were unable to identify S. delphini to the species level, a function of its omission from their databases, but could identify isolates to the SIG level with various degrees of success. However, all automated systems misidentified at least one isolate as Staphylococcus aureus. One matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) system was able to identify S. delphini to the species level, suggesting that MALDI-TOF MS is the best option for distinguishing members of the SIG. With the exception of S. pseudintermedius, it is unclear if other SIG members should be routinely identified to the species level; however, as our understanding of their role in animal and human diseases increases, it may be necessary and important to do so.

Some Experiments and Observations on the Longevity of Diphyllobothrium Infections

1936 ◽  
Vol 14 (3) ◽  
pp. 127-130 ◽  
Author(s):  
R. T. Leiper
Keyword(s):  
Adult Life ◽  
Infected Fish ◽  
Human Infection ◽  
Natural Occurrence ◽  
Natural Area ◽  
North American Continent ◽  
The North ◽  
History Of ◽  
Typical Instance ◽  
Diphyllobothrium Latum

In an article on “The Longevity of Diphyllobothrium latum” published in 1935 in the “Recueil des Travaux dédié au 25-me Anniversaire Scientifique du Professeur Eugène Paviosky 1909−1934”, it is suggested that present day conceptions regarding the longevity of this parasite are erroneous and that multiple successive infections are frequently attributed to a single long-lived specimen. Ward gives a detailed review and analysis of the evidence hitherto published both in general works and special monographs and cites as specially important the history of the occurrence of this species on the North American continent. He points out that the age of the parasite is regularly based on the statement that the host had not been in an infected region for the period indicated. To this statement, Ward puts forward the objections that the distribution of the parasite and the natural occurrence of plerocercoid carrying fish are far more extensive than was formerly suspected and, further, that infected fish are distributed commercially as food to regions far outside their natural area of distribution. He also refers to certain records which seem to indicate that there is a “period of inactivity” during the adult life of the parasite and suggests that its alleged occurrence throws doubt upon the supposed longevity of the parasite. In support of this contention, he cites, as a typical instance, a case of human infection with Diphyllobothrium latum reported by me (Leiper, 1928) as a “cryptic infection”; regarding which he erroneously states that I believed was “latent” for 5 years.

FUSARIUM-ID v.3.0: An updated, downloadable resource for Fusarium species identification

Plant Disease ◽  
2021 ◽  
Author(s):  
Terry Torres-Cruz ◽  
Briana Whitaker ◽  
Robert Proctor ◽  
Kirk Broders ◽  
Imane Laraba ◽  
...  
Keyword(s):  
Sequence Data ◽  
Safety Concern ◽  
Fusarium Species ◽  
Elongation Factor ◽  
Sequence Database ◽  
Accurate Identification ◽  
Dna Sequence Data ◽  
Species Complexes ◽  
Marker Loci ◽  
Feed Safety

Species within Fusarium are of global agricultural, medical, and food/feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID (http://isolate.fusariumdb.org/) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ~680 bp 5' portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v.1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely-available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.

scholarly journals Emergence of Epidemic Multidrug-Resistant Enterococcus faecium from Animal and Commensal Strains

mBio ◽  
2013 ◽  
Vol 4 (4) ◽  
Author(s):  
François Lebreton ◽  
Willem van Schaik ◽  
Abigail Manson McGuire ◽  
Paul Godfrey ◽  
Allison Griggs ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Sequence Data ◽  
Mobile Element ◽  
Multidrug Resistant ◽  
Human Infection ◽  
Animal Origin ◽  
Loss Of Function ◽  
Content Type ◽  
Hospital Acquired Infection ◽  
Hospital Acquired

ABSTRACTEnterococcus faecium, natively a gut commensal organism, emerged as a leading cause of multidrug-resistant hospital-acquired infection in the 1980s. As the living record of its adaptation to changes in habitat, we sequenced the genomes of 51 strains, isolated from various ecological environments, to understand howE. faeciumemerged as a leading hospital pathogen. Because of the scale and diversity of the sampled strains, we were able to resolve the lineage responsible for epidemic, multidrug-resistant human infection from other strains and to measure the evolutionary distances between groups. We found that the epidemic hospital-adapted lineage is rapidly evolving and emerged approximately 75 years ago, concomitant with the introduction of antibiotics, from a population that included the majority of animal strains, and not from human commensal lines. We further found that the lineage that included most strains of animal origin diverged from the main human commensal line approximately 3,000 years ago, a time that corresponds to increasing urbanization of humans, development of hygienic practices, and domestication of animals, which we speculate contributed to their ecological separation. Each bifurcation was accompanied by the acquisition of new metabolic capabilities and colonization traits on mobile elements and the loss of function and genome remodeling associated with mobile element insertion and movement. As a result, diversity within the species, in terms of sequence divergence as well as gene content, spans a range usually associated with speciation.IMPORTANCEEnterococci, in particular vancomycin-resistantEnterococcus faecium, recently emerged as a leading cause of hospital-acquired infection worldwide. In this study, we examined genome sequence data to understand the bacterial adaptations that accompanied this transformation from microbes that existed for eons as members of host microbiota. We observed changes in the genomes that paralleled changes in human behavior. An initial bifurcation within the species appears to have occurred at a time that corresponds to the urbanization of humans and domestication of animals, and a more recent bifurcation parallels the introduction of antibiotics in medicine and agriculture. In response to the opportunity to fill niches associated with changes in human activity, a rapidly evolving lineage emerged, a lineage responsible for the vast majority of multidrug-resistantE. faeciuminfections.

scholarly journals First Report of Leptosphaeria biglobosa (Blackleg) on Brassica oleracea (Cabbage) in Mexico

Plant Disease ◽  
2010 ◽  
Vol 94 (6) ◽  
pp. 791-791 ◽  
Author(s):  
A. Dilmaghani ◽  
M. H. Balesdent ◽  
T. Rouxel ◽  
O. Moreno-Rico
Keyword(s):  
Brassica Oleracea ◽  
Sequence Data ◽  
Leptosphaeria Maculans ◽  
The United States ◽  
Internal Transcribed Spacers ◽  
First Report ◽  
5.8S Rdna ◽  
Single Location ◽  
Leptosphaeria Biglobosa ◽  
Β Tubulin

Broccoli (Brassica oleracea var. italica), cauliflower (B. oleracea var. botrytis), and cabbage (B. oleracea var. capitata) have been grown in central Mexico since 1970, with 21,000 ha cropped in 2001. In contrast, areas grown with oilseed rape (B. napus) are very limited in Mexico (<8,000 ha). Blackleg, a destructive disease of B. napus in most parts of the world, was first observed in Mexico in Zacatecas and Aguascalientes in 1988 on B. oleracea, causing as much as 70% yield loss. A species complex of two closely related Dothideomycete species, Leptosphaeria maculans and L. biglobosa, is associated with this disease of crucifers (1), but leaf symptoms on susceptible plants are different, with L. maculans typically causing >15-mm pale gray lesions with numerous pycnidia, whereas L. biglobosa causes dark and smaller lesions only containing a few pycnidia. Having a similar epidemiology, both species can be present on the same plants at the same time, and symptom confusion can occur as a function of the physiological condition of the plant or expression of plant resistance responses. A total of 209 isolates from symptomatic B. oleracea leaves were collected from three fields in central states of Mexico (58 to 71 isolates per location). All leaves showed similar symptoms, including a 10- to 15-mm tissue collapse with an occasional dark margin. Cotyledons of seven B. napus differentials were inoculated with conidia of all the isolates as described by Dilmaghani et al. (1). Two hundred isolates caused tissue collapse typical of L. maculans. However, nine obtained from white cabbage in a single location in Aguascalientes caused <5-mm dark lesions. When inoculated onto cotyledons of three B. oleracea genotypes commonly grown in Mexico (cvs. Domador, Monaco, and Iron Man), the nine isolates caused a range of symptoms characterized by tissue collapse (maximum 10 to 15 mm), showing the presence of patches of black necrotic spots within the collapse. The occasional presence of a few pycnidia allowed us to reisolate the fungus for molecular identification. ITS1-5.8S-ITS2, (internal transcribed spacers and 5.8S rDNA), actin, and β-tubulin sequences were obtained as described previously (4). Multiple gene genealogies based on these sequence data showed two subclades of L. biglobosa: L. biglobosa ‘occiaustralensis’ (one isolate; ITS [AM410082], actin [AM410084], and β-tubulin [AM410083]) and L. biglobosa ‘canadensis’ (eight isolates; ITS [AJ550868], actin [AY748956], and β-tubulin [AY749004]) (3,4), which were previously described on B. napus in the United States, Canada, and Chile. To our knowledge, this is the first report of L. biglobosa in Mexico. Previously, this species has only been reported once on B. oleracea without discrimination into subclades (2). In the Aguascalientes sampling, 24% of the isolates were L. biglobosa, similar to Canadian locations where this species is still common as compared with L. maculans (1). The large proportion of sampled L. biglobosa ‘canadensis’, highlights the prevalence of this subclade throughout the American continent (1). References: (1) A. Dilmaghani et al. Plant Pathol. 58:1044, 2009. (2) E. Koch et al. Mol. Plant-Microbe Interact. 4:341, 1991. (3) E. Mendes-Pereira et al. Mycol Res. 107:1287, 2003. (4) L. Vincenot et al. Phytopathology 98:321, 2008.

scholarly journals Sensitive detection of DNA contamination in tumor samples via microhaplotypes

2020 ◽  
Author(s):  
Brett Whitty ◽  
John F. Thompson
Keyword(s):  
Sequence Data ◽  
Accurate Determination ◽  
Sensitive Detection ◽  
European Ancestry ◽  
Somatic Variation ◽  
Dna Mixtures ◽  
Accurate Identification ◽  
Sample Contamination ◽  
Dna Contamination ◽  
Low Levels

AbstractBackgroundLow levels of sample contamination can have disastrous effects on the accurate identification of somatic variation in tumor samples. Detection of sample contamination in DNA is generally based on observation of low frequency variants that suggest more than a single source of DNA is present. This strategy works with standard DNA samples but is especially problematic in solid tumor FFPE samples because there can be huge variations in allele frequency (AF) due to massive copy number changes arising from large gains and losses across the genome. The tremendously variable allele frequencies make detection of contamination challenging. A method not based on individual AF is needed for accurate determination of whether a sample is contaminated and to what degree.MethodsWe used microhaplotypes to determine whether sample contamination is present. Microhaplotypes are sets of variants on the same sequencing read that can be unambiguously phased. Instead of measuring AF, the number and frequency of microhaplotypes is determined. Contamination detection becomes based on fundamental genomic properties, linkage disequilibrium (LD) and the diploid nature of human DNA, rather than variant frequencies. We optimized microhaplotype content based on 164 single nucleotide variant sets located in genes already sequenced within a cancer panel. Thus, contamination detection uses existing sequence data and does not require sequencing of any extraneous regions. The content is chosen based on LD data from the 1000 Genomes Project to be ancestry agnostic, providing the same sensitivity for contamination detection with samples from individuals of African, East Asian, and European ancestry.ResultsDetection of contamination at 1% and below is possible using this design. The methods described here can also be extended to other DNA mixtures such as forensic and non-invasive prenatal testing samples where DNA mixes of 1% or less can be similarly detected.ConclusionsThe microhaplotype method allows sensitive detection of DNA contamination in FFPE tumor samples. These methods provide a foundation for examining DNA mixtures in a variety of contexts. With the appropriate panels and high sequencing depth, low levels of secondary DNA can be detected and this can be valuable in a variety of applications.

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