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Fulltext Pathogenic waterborne free-living amoebae: An update from selected Southeast Asian countries

Abdul Majid MA, Mahboob T, Mong BG, Jaturas N, Richard RL, Tian-Chye T, et al.

PLoS One, 2017;12(2):e0169448.
PMID: 28212409 DOI: 10.1371/journal.pone.0169448

Data on the distribution of free-living amoebae is still lacking especially in Southeast Asian region. The aquatic environment revealed a high occurrence of free-living amoebae (FLA) due to its suitable condition and availability of food source, which subsequently causes infection to humans. A total of 94 water samples consisted of both treated and untreated from Laos (31), Myanmar (42), and Singapore (21) were investigated for the presence of pathogenic FLA. Each water sample was filtered and cultured onto non-nutrient agar seeded with live suspension of Escherichia coli and incubated at room temperature. Morphological identification was conducted for both trophozoites and cysts via microscopic stains (Giemsa and immunofluorescence). The presence of Naegleria-like structures was the most frequently encountered in both treated and untreated water samples, followed by Acanthamoeba-like and Vermamoeba-like features. To identify the pathogenic isolates, species-specific primer sets were applied for molecular identification of Acanthamoeba, Naegleria, and Vermamoeba. The pathogenic species of Acanthamoeba lenticulata and A. triangularis were detected from untreated water samples, while Vermamoeba vermiformis was found in both treated and untreated water samples. Our results suggested that poor water quality as well as inadequate maintenance and treatment might be the cause of this alarming problem since chlorine disinfection is ineffective in eradicating these amoebas in treated water samples. Regular monitoring and examination of water qualities are necessary in order to control the growth, hence, further preventing the widespread of FLA infections among the public.

Matched MeSH terms: Phylogeny
Fulltext Rare Elizabethkingia anophelis meningitis case in a Danish male

Nielsen HL, Tarpgaard IH, Fuglsang-Damgaard D, Thomsen PK, Brisse S, Dalager-Pedersen M

JMM Case Rep, 2018 Aug;5(8):e005163.
PMID: 30323938 DOI: 10.1099/jmmcr.0.005163

Introduction: Elizabethkingia anophelis is a Gram-negative, aerobic, non-motile rod belonging to the family Flavobacteriaceae. Over the last 5 years, it has emerged as an opportunistic human pathogen involved in neonatal meningitis and sepsis, as well as nosocomial outbreaks. It has been isolated from the midgut of the Anopheles gambiae mosquito, but there is no evidence for a role of the mosquito in human infections, and very little is known regarding the routes of transmission to humans. Recent studies, primarily from South-East Asia, suggest that E. anophelis, and not Elizabethkingia meningoseptica, is the predominant human pathogen of this genus. However, identification to the species level has been difficult due to the limitations of the current MALDI-TOF MS (matrix-associated laser desorption ionization-time of flight MS) systems for correct species identification.
Case presentation: Here, we present a rare case of E. anophelis meningitis in a Danish male, who had a travel exposure to Malaysia 7 weeks before hospitalization. A multidrug-resistant Elizabethkingia species was isolated from blood and cerebrospinal fluid, and genomic sequencing was used to characterize the phylogenetic position of the isolate, which was determined as associated with previously described sublineage 11. The patient was successfully treated with intravenous moxifloxacin and rifampicin for 2 weeks with no major sequelae, but we did not find the source of transmission.
Conclusion: All clinical microbiologists should be aware of the present limitations of the MALDI-TOF MS systems for correct species identification, and therefore we recommend the use of genome sequencing for the correct identification at the species and sublineage level.

Matched MeSH terms: Phylogeny
Fulltext Mathematical modelling of molybdenum reduction to Mo-blue by a cyanide-degrading bacterium

Yakasai, H.M., Karamba, K.I., Yasid, N.A., Abd. Rahman, F., Shukor, M.Y., Halmi, M.I.E.

Bioremediation Science and Technology Research, 2016;4(2):1-5.
MyJurnal

Molybdenum, an emerging pollutant, has being demonstrated recently to be toxic to
spermatogenesis in several animal model systems. Metal mines especially gold mine often use
cyanide and hence isolation of metal-reducing and cyanide-degrading bacteria can be useful for
the bioremediation of these pollutants. Preliminary screening shows that three cyanide-degrading
bacteria were able to reduce molybdenum to molybdenum blue (Mo-blue) when grown on a
molybdate low phosphate minimal salts media. Phylogenetic analyses of the 16S rRNA gene of
the best reducer indicates that it belongs to the Serratia genus. A variety of mathematical models
such as logistic, Gompertz, Richards, Schnute, Baranyi-Roberts, von Bertalanffy, Buchanan
three-phase and Huang were used to model molybdenum reduction, and the best model based on
statistical analysis was modified Gompertz with lowest values for RMSE and AICc, highest
adjusted R2 values, with Bias Factor and Accuracy Factor nearest to unity (1.0). The reduction
constants obtained from the model will be used to carry out secondary modelling to study the
effect of various parameters such as substrate, pH and temperature to molybdenum reduction.

Matched MeSH terms: Phylogeny
Fulltext Isolation and characterization of a metal-reducing Pseudomonas sp. strain 135 with amide-degrading capability

Yakasai, M.H., Rahman, M.F., Khayat, M.E., Shukor, M.Y., Shamaan, N.A., Rahim, M.B.H.A.

Bioremediation Science and Technology Research, 2017;5(2):32-38.
MyJurnal

The presence of both heavy metals and organic xenobiotic pollutants in a contaminated site
justifies the application of either a multitude of microbial degraders or microorganisms having
the capacity to detoxify a number of pollutants at the same time. Molybdenum is an essential
heavy metal that is toxic to ruminants at a high level. Ruminants such as cow and goats
experience severe hypocuprosis leading to scouring and death at a concentration as low as
several parts per million. In this study, a molybdenum-reducing bacterium with amide-degrading
capacity has been isolated from contaminated soils. The bacterium, using glucose as the best
electron donor reduces molybdenum in the form of sodium molybdate to molybdenum blue. The
maximal pH reduction occurs between 6.0 and 6.3, and the bacterium showed an excellent
reduction in temperatures between 25 and 40 oC. The reduction was maximal at molybdate
concentrations of between 15 and 25 mM. Molybdenum reduction incidentally was inhibited by
several toxic heavy metals. Other carbon sources including toxic xenobiotics such as amides
were screened for their ability to support molybdate reduction. Of all the amides, only
acrylamide can support molybdenum reduction. The other amides; such as acetamide and
propionamide can support growth. Analysis using phylogenetic analysis resulted in a tentative
identification of the bacterium as Pseudomonas sp. strain 135. This bacterium is essential in
remediating sites contaminated with molybdenum, especially in agricultural soil co-contaminated
with acrylamide, a known soil stabilizer.

Matched MeSH terms: Phylogeny
Fulltext Authenticity Testing and Detection of Eurycoma longifolia in Commercial Herbal Products Using Bar-High Resolution Melting Analysis

Fadzil NF, Wagiran A, Mohd Salleh F, Abdullah S, Mohd Izham NH

Genes (Basel), 2018 Aug 12;9(8).
PMID: 30103564 DOI: 10.3390/genes9080408

The present study demonstrated High Resolution Melting (HRM) analysis combined with DNA barcode (Bar-HRM) as a fast and highly sensitive technique for detecting adulterants in Eurycoma longifolia commercial herbal products. Targeting the DNA barcoding of the chloroplastic region-ribulose biphosphate carboxylase large chain (rbcL) and the nuclear ribosomal region- internal transcribed spacer 2 (ITS2), PCR amplification and HRM analysis using saturated Eva green dye as the source of fluorescence signals, was accomplished by employing a real-time cycler. The results were further validated by sequencing to identify unknown sequence from Genbank database and to generate phylogenetic tree using neighbour joint (NJ) analysis. Both of the DNA markers exhibited a distinguishable melting temperature and shape of the normalised curve between the reference and the adulterants. In the case of species identification, ITS2 was more successful in differentiating between species. Additionally, detection of admixture sample containing small traces of targeted E. longifolia DNA (w/v) can be detected as low as 5% for rbcL and less than 1% for ITS2, proving the sensitivity and versatility of the HRM analysis. In conclusion, the Bar-HRM analysis is a fast and reliable technique that can effectively detect adulterants in herbal products. Therefore, this will be beneficial for regulatory agencies in order to regulate food safety issues.

Matched MeSH terms: Phylogeny
New perspectives of Lactobacillus plantarum as a probiotic: The gut-heart-brain axis

Liu YW, Liong MT, Tsai YC

J Microbiol, 2018 Sep;56(9):601-613.
PMID: 30141154 DOI: 10.1007/s12275-018-8079-2

Lactobacillus plantarum is a non-gas-producing lactic acid bacterium that is generally regarded as safe (GRAS) with Qualified Presumption of Safety (QPS) status. Although traditionally used for dairy, meat and vegetable fermentation, L. plantarum is gaining increasing significance as a probiotic. With the newly acclaimed gut-heart-brain axis, strains of L. plantarum have proven to be a valuable species for the development of probiotics, with various beneficial effects on gut health, metabolic disorders and brain health. In this review, the classification and taxonomy, and the relation of these with safety aspects are introduced. Characteristics of L. plantarum to fulfill the criteria as a probiotic are discussed. Emphasis are also given to the beneficial functions of L. plantarum in gut disorders such as inflammatory bowel diseases, metabolic syndromes, dyslipidemia, hypercholesteromia, obesity, and diabetes, and brain health aspects involving psychological disorders.

Matched MeSH terms: Phylogeny
[Laboratory diagnosis and molecular tracing of dengue bordline cases in Henan Province, 2017]

Du YH, Li Y, Wang RL, Wang HF, Su J, Xu BL, et al.

Zhonghua Yu Fang Yi Xue Za Zhi, 2018 Nov 06;52(11):1164-1167.
PMID: 30419702 DOI: 10.3760/cma.j.issn.0253-9624.2018.11.013

Objective: To confirm the laboratory diagnosis of dengue bordline cases reported in Henan Province and trace its origin from molecular level in 2017. Methods: The study samples were blood samples (3-5 ml), which came from 8 suspected cases of dengue fever reported in the 2017 direct reporting system of Henan provincial infectious disease monitoring network. Meanwhile, case investigation was conducted according to National dengue fever surveillance programme. Serum were separated from blood samples and tested for Dengue NS1 antigen, IgM & IgG antibodies, and dengue RNA. According to dengue diagnosis criteria, confirmed cases were identified by testing results. Samples carried dengue RNA performed for real-time PCR genotyping and amplification of E gene. Then, the amplicons were sequenced and homological and phylogenetic analyses were constructed. Results: 8 serum samples of suspected dengue cases were collected in Henan Province, 2017. Six of them were diagnosed as dengue confirmed cases. All the dengue confirmed cases belonged to outside imported cases, 5 of them were positive by dengue RNA testing. Genotyping results showed there were 1 DENV1 case, 2 DENV2 cases and 2 DENV3 cases. A DENV2 case and a DENV3 case of this study were traced its origin successfully. The sequence of Pakistan imported DENV2 case belongs to cosmopolitan genotype, which was the most consistent with Pakistan's DENV2 KJ010186 in 2013 (identity 99.0%). The sequence of Malaysia imported DENV3 case belongs to genotype I, which was the most consistent with Singapore's DENV3 KX224276 in 2014(identity 99.0%). Conclusion: The laboratory diagnosis and molecular traceability of dengue cases in Henan Province in 2017 confirmed that all cases were imported and did not cause local epidemics.

Matched MeSH terms: Phylogeny
Review of the huntsman spider genus Rhitymna Simon, 1897 (Araneae: Sparassidae)

Jäger P

Zootaxa, 2019 Feb 26;4560(3):zootaxa.4560.3.2.
PMID: 31716566 DOI: 10.11646/zootaxa.4560.3.2

The genus Rhitymna Simon, 1897 is revised by means of new material. Four new species are described: R. gerdmangel spec. nov. (Thailand, Malaysia; male, female), R. merianae spec. nov. (Indonesia: Bali; male), R. flores spec. nov. (Indonesia: Flores; male, female), R. senckenbergi spec. nov. (Philippines; male). The male of R. plana Jäger, 2003 and the female of R. tangi Quan Liu, 2012 are described for the first time. Rhitymna simoni Jäger, 2003 is recognised as junior synonym of R. cursor (Thorell, 1894) comb. nov., the latter transferred from the genus Olios Walckenaer, 1837. New records are given for further Rhitymna species, among them new country or island records for R. verruca (Wang, 1991) (Thailand), R. tangi Quan Liu, 2012 (Laos), R. plana Jäger, 2003 (Cambodia), R. pinangensis (Thorell, 1891) (Thailand), R. deelemanae Jäger, 2003 (Bali). The number of cheliceral bristles close to the fang base is recognised as size dependent, therefore without true phylogenetic signal. Two main types of copulatory organs within the genus are recognised and discussed. R. gerdmangel spec. nov. has a special biology as it lives exclusively in bamboo. Holes made by beetles or woodpeckers are used to enter the bamboo stem. Spiders hide during the day and lay their eggs in bamboo internodes.

Matched MeSH terms: Phylogeny
First description of the tadpole of Theloderma ryabovi Orlov, Dutta, Ghate et Kent, 2006 (Anura: Rhacophoridae), an endemic mossy frog from Vietnam

Kropachev II, Orlov NL, Ostroshabov AA, Nguyen TT

Zootaxa, 2019 Aug 15;4657(1):zootaxa.4657.1.13.
PMID: 31716807 DOI: 10.11646/zootaxa.4657.1.13

To date, 26 species of Theloderma have been described and all are distributed throughout Southeast Asia from Assam in northeastern India to Myanmar, Indochina, the Malay Peninsula, and the islands of the Greater Sundas: Sumatra and Borneo (Frost 2019). The tadpoles of only 12 species have been described and published: T. asperum (Boulenger); T. auratum Poyarkov, Kropachev, Gogoleva Orlov; T. bicolor (Bourret); T. corticale (Boulenger); T. gordoni Taylor; T. horridum (Boulenger); T. leave (Smith); T. moloch (Annandale); T. nebulosum Rowley, Le, Hoang, Dau Cao; T. palliatum Rowley, Le, Hoang, Dau Cao; T. stellatum Taylor; T. vietnamense Poyarkov, Orlov, Moiseeva, Pawangkhanant, Ruangsuwan, Vassilieva, Galoyan, Nguyen Gogoleva (Boulenger 1903; Annandale 1912; Wassersug et al. 1981; Inger et al. 1999; Leong Lim 2003; Inthara et al. 2005; Rowley et al. 2011; Gawor et al. 2012; Orlov et al. 2012; Poyarkov et al. 2015; Kropachev et al. 2018).

Matched MeSH terms: Phylogeny
Occurrence and molecular characterisation of Acanthamoeba isolated from recreational hot springs in Malaysia: evidence of pathogenic potential

Mohd Hussain RH, Ishak AR, Abdul Ghani MK, Ahmed Khan N, Siddiqui R, Shahrul Anuar T

J Water Health, 2019 Oct;17(5):813-825.
PMID: 31638031 DOI: 10.2166/wh.2019.214

This study aimed to identify the Acanthamoeba genotypes and their pathogenic potential in five recreational hot springs in Peninsular Malaysia. Fifty water samples were collected between April and September 2018. Physical parameters of water quality were measured in situ while chemical and microbiological analyses were performed in the laboratory. All samples were filtered through the nitrocellulose membrane and tested for Acanthamoeba using both cultivation and polymerase chain reaction (PCR) by targeting the 18S ribosomal RNA gene. The pathogenic potential of all positive isolates was identified using thermo- and osmotolerance tests. Thirty-eight (76.0%) samples were positive for Acanthamoeba. Water temperature (P = 0.035), chemical oxygen demand (P = 0.026), sulphate (P = 0.002) and Escherichia coli (P < 0.001) were found to be significantly correlated with the presence of Acanthamoeba. Phylogenetic analysis revealed that 24 samples belonged to genotype T4, nine (T15), two (T3) and one from each genotype T5, T11 and T17. Thermo- and osmotolerance tests showed that 6 (15.79%) of the Acanthamoeba strains were highly pathogenic. The existence of Acanthamoeba in recreational hot springs should be considered as a health threat among the public especially for high-risk people. Periodic surveillance of hot spring waters and posting warning signs by health authorities is recommended to prevent disease related to pathogenic Acanthamoeba.

Matched MeSH terms: Phylogeny
Fulltext Isolation and Characterization of a Novel Pathogenic Strain of Ehrlichia minasensis

Moura de Aguiar D, Pessoa Araújo Junior J, Nakazato L, Bard E, Aguilar-Bultet L, Vorimore F, et al.

Microorganisms, 2019 Nov 05;7(11).
PMID: 31694172 DOI: 10.3390/microorganisms7110528

The genus Ehrlichia is composed of tick-borne obligate intracellular gram-negative alphaproteobacteria of the family Anaplasmataceae. Ehrlichia includes important pathogens affecting canids (E. canis, E. chaffeensis, and E. ewingii), rodents (E. muris), and ruminants (E. ruminantium). Ehrlichiaminasensis, an Ehrlichia closely related to E. canis, was initially reported in Canada and Brazil. This bacterium has now been reported in Pakistan, Malaysia, China, Ethiopia, South Africa, and the Mediterranean island of Corsica, suggesting that E. minasensis has a wide geographical distribution. Previously, E. minasensis was found to cause clinical ehrlichiosis in an experimentally infected calf. The type strain E. minasensis UFMG-EV was successfully isolated from Rhipicephalus microplus ticks and propagated in the tick embryonic cell line of Ixodes scapularis (IDE8). However, the isolation and propagation of E. minasensis strains from cattle has remained elusive. In this study, the E. minasensis strain Cuiabá was isolated from an eight-month-old male calf of Holstein breed that was naturally infected with the bacterium. The calf presented clinical signs and hematological parameters of bovine ehrlichiosis. The in vitro culture of the agent was established in the canine cell line DH82. Ehrlichial morulae were observed using light and electron microscopy within DH82 cells. Total DNA was extracted, and the full genome of the E. minasensis strain Cuiabá was sequenced. A core-genome-based phylogenetic tree of Ehrlichia spp. and Anaplasma spp. confirmed that E. minasensis is a sister taxa of E. canis. A comparison of functional categories among Ehrlichia showed that E. minasensis has significantly less genes in the 'clustering-based subsystems' category, which includes functionally coupled genes for which the functional attributes are not well understood. Results strongly suggest that E. minasensis is a novel pathogen infecting cattle. The epidemiology of this Ehrlichia deserves further attention because these bacteria could be an overlooked cause of tick-borne bovine ehrlichiosis, with a wide distribution.

Matched MeSH terms: Phylogeny
DNA polymorphism of D1S80 locus in modern Malay sample population of Sarawak

Hairul Azman Roslan, Nur Hafizah Azizan, Rosmawati Saat

Sains Malaysiana, 2009;38.

The molecular genetic marker, minisatellite locus D1S80 (1p35-p36), is a highly polymorphic variable number of tandem repeats (VNTR). Its polymorphic nature allows for phylogenetic studies, forensic analysis, genetic maps construction and paternity testing to be performed. A study of the hypervariable locus D1S80 was conducted to determine the allele frequency and distribution of this locus in modern Malay in Sarawak population. The polymerase chain reaction technique was employed and results were analysed on polyacrylamide gel. A total of seventy-six DNA samples of unrelated Malay individuals in UNIMAS were collected and examined. The VNTR analysis of the D1S80 locus demonstrated the presence of 17 alleles in the Malay population. Allele with the size of 577 bp (27 repeats) was determined to be the most common in the sample population with the frequency of 0.1641, followed by allele with the size of 561 bp (26 repeats) and 529 bp (24 repeats) whose frequency is 0.1172 and 0.1094, respectively. The smallest allele is allele with the size of 465 bp (20 repeats) whereas the largest is allele with the size of 753 bp (38 repeats). The sample population exhibited 57.8% heterozygosity.

Matched MeSH terms: Phylogeny
Molecular phylogeny of holothuria (mertensiothuria) leucospilota (Brandt 1835) as inferred from cytochrome C oxidase I mitochondrial DNA gene sequences

Hajar Fauzan Ahmad, Mohd Hanafi Anua, Mohd Yaman Idris, Aisyah Mohamed Rehan, Ridzwan Hashim, Usup G, et al.

Sains Malaysiana, 2011;40.

Holothuria (Mertensiothuria) leucospilota (Brandt 1835), white threads fish or locally known as bat puntil is currently considered as the most abundant sea cucumber species in Malaysia. This study aimed to generate the genetic profile of H. leucospilota from Malaysia and then to determine the phylogenetic relationship between H. leucospilota and other members of genus Holothuria using partial sequences of cytochrome c oxidase I (COI) mitochondrial DNA (mtDNA) gene. In this study, specimens of H. leucospilota were collected from Intan Besar Island, Langkawi, Kedah Darul Aman in the west coast of Peninsular Malaysia. Three main methods namely neighbour joining, maximum parsimony and maximum likelihood were used for the phylogenetic tree reconstruction. Tree topologies showed that H. leucospilota has its own monophyletic clade clearly distinct from the other species. The pairwise genetic distance calculated further supported these findings. In addition, the results also should that the COI mtDNA gene is capable to unravel the phylogenetic relationship of H. leucospilota.

Matched MeSH terms: Phylogeny
Revision of Acanthotaenia von Linstow, 1903 (Cestoda: Proteocephalidae), parasites of monitors (Varanus spp.), based on morphological and molecular data

de Chambrier A, Brabec J, Tran BT, Scholz T

Parasitol Res, 2019 Jun;118(6):1761-1783.
PMID: 31065829 DOI: 10.1007/s00436-019-06326-6

A morphological and molecular phylogenetic study of proteocephalid tapeworms of the genus Acanthotaenia von Linstow, 1903, parasites of monitors (Varanidae), was carried out. The type species, A. shipleyi von Linstow, 1903, which was originally described based on an immature specimen from Sri Lanka, is redescribed based on new material from the type host, Varanus salvator, in Sri Lanka, Malaysia, and Vietnam, and its neotype is designated. In addition, Acanthotaenia susanae n. sp. is described from Varanus nebulosus in Vietnam. The new species differs from congeners by the large size of the scolex, width of the rostellum and the number of testes. New molecular data (sequences of lsrDNA and cox1) revealed Acanthotaenia paraphyletic with the inclusion of Australotaenia bunthangi de Chambrier & Scholz, 2012, a parasite of Enhydris enhydris (Ophidia: Homalopsidae) in Cambodia. Molecular data confirm a wide distribution of A. shipleyi (isolates from Malaysia and Vietnam were almost identical) and indicate a strict host specificity (oioxeny) of individual species of the genus. Type specimens of four species made it possible to supplement their morphological descriptions. A survey of all species of Acanthotaenia recognised as valid is presented and the following taxonomic changes are proposed: Acanthotaenia pythonis Wahid, 1968 described from the green python, Morelia viridis, in a zoo, is transferred to Kapsulotaenia as Kapsulotaenia pythonis (Wahid, 1968) n. comb., because it possesses intrauterine eggs grouped in capsules. Acanthotaenia gracilis (Beddard, 1913) from Varanus varius in Australia is considered to be species inquirenda because its original descriptions did not contain sufficient data for adequate circumscription and differentiation from congeners and type material was not available. Generic diagnosis of Acanthotaenia is amended and a key to its seven species is provided.

Matched MeSH terms: Phylogeny
Molecular Mitochondrial DNA and radiographic approaches for human archaeology identification

Rus Dina Rus Din, Shahrul Hisham Zainal Ariffin, Sahidan Senafi, Rohaya Megat Abdul Wahab, Intan Zarina Zainol Abidin

Sains Malaysiana, 2014;43:1523-1535.

Ancient remains are considered very valuable artefacts, as they allow for the study of ancient cultures, phylogeny, evolution and the reconstruction of demographic history. To obtain all the information contained within remains, the investigation of such samples requires the expertise and various techniques from multiple fields of study. The present review focuses on the molecular biology and radiographic approaches used to identify ancient samples. Studies of ancient remains face various limitations; for example, the quality and quantity of the ancient samples can affect the difficulty of the investigations. Due to these limitations, new sophisticated techniques are being introduced to replace the earlier conventional techniques. A search was conducted using PubMed, Scopus, Science Direct and Science Finder to provide a new and timely review on the molecular mitochondrial DNA and radiographic analysis for human archaeology identification. The present review has determined that molecular biological approaches are very accurate and useful for the use in the ancestral determination of incomplete specimens, whereas observations of the dental pulp chamber are suitable for age at death estimations in both adults and children. However, these techniques are expensive and require expert personnel. Therefore, conventional approaches remain the favourite methods of most institutions, especially in Asia.

Matched MeSH terms: Phylogeny
Phylogenetic relationships within the genus holothuria inferred from 16S mitochondiral rRNA gene sequences

Kamarul Rahim Kamarudin, ‘Aisyah Mohamed Rehan, Ridzwan Hashim, Usup G, Maryam Mohamed Rehan

Sains Malaysiana, 2016;45:1079-1087.

This study aimed to resolve the taxonomic status of a morphologically undetermined sea cucumber species of order Apodida
from Malaysia (GenBank accession no.: FJ223867) using partial 16S mitochondrial rRNA gene sequences and subsequently
to determine the validity of morphological taxonomy of Holothuria species into its current subgenera. The undetermined
species clustered with all taxa of Holothuria in previous study. Phylogenetic analyses using maximum parsimony and
Bayesian methods suggest that the undetermined species was genetically closer to Holothuria (Lessonothuria) pardalis and
Holothuria (Acanthotrapeza) coluber; and its position in both phylogenetic trees further suggests its status as a Holothuria
taxon. Subgenera of Holothuria, Merthensiothuria and Metriatyla are monophyletic with strong bootstrap supports and
posterior probabilities of clades, thus strengthening their morphological taxonomies. Nonetheless, the non-monophyly of
subgenera of Halodeima, Microthele and Platyperona suggests a requirement for their taxonomic revisions using integrative
taxonomy. The status of Holothuria (Halodeima) edulis subgroups in the maximum parsimony and Bayesian trees is
indistinct and further taxonomic revisions are necessary. In terms of sister relationship, both phylogenetic trees suggest
that subgenus Holothuria is a sister taxon of subgenus Roweothuria while the other sister relationships were unclear due
to the undetermined species, paraphyly and polyphyly of a number of subgenera. Further studies with more specimens of
genus Holothuria from broader geographical locations and various mtDNA genes along with morphological approaches
may facilitate to provide better insights into the molecular phylogeny of subgenera of Holothuria.

Matched MeSH terms: Phylogeny
Phylogeny of sea cucumber (Echinodermata: Holothuroidea) as inferred from 16S mitochondrial rRNa gene sequences

Kamarul Rahim Kamarudin, Ridzwan Hashim, Usup G

Sains Malaysiana, 2010;39:209-218.

This study aimed to determine phylogenetic relationship between and among selected species of sea cucumbers (Echinodermata: Holothuroidea) using 16S mitochondrial ribosomal RNA (rRNA) gene. Phylogenetic analyses of 37 partial sequences of 16S mitochondrial rRNA gene using three main methods namely neighbour joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) showed the presence of five main genera of sea cucumbers: Molpadia from order Molpadiida and four genera of order Aspidochirotida namely Holothuria, Stichopus, Bohadschia and Actinopyga. All of the 17 species obtained from Malaysia distributed among the main genera except within Actinopyga. Interestingly, Holothuria excellens was out of Holothuria group causing Holothuria to be paraphyletic. High bootstrap value and consistent clustering made Molpadia, Stichopus, Bohadschia and Actinopyga monophyletic. The relationship of Actinopyga with the other genera was unclarified and Stichopus was sister to Molpadia. The latter finding caused the resolution at order level unclear. The pairwise genetic distance calculated using Kimura 2-parameter model further supported and verified findings from the phylogenetic trees. Further studies with more samples and different mitochondrial DNA genes need to be done to get a better view and verification on the molecular phylogeny of sea cucumbers.

Matched MeSH terms: Phylogeny
Molecular identification of Eimeria hestermani and Eimeria prionotemni from a red-necked wallaby (Macropodidae; Macropus rufogriseus) in Japan

Ekawasti F, Kitagawa K, Domae H, Wardhana AH, Shibahara T, Uni S, et al.

Parasitol Res, 2020 Apr;119(4):1271-1279.
PMID: 32072327 DOI: 10.1007/s00436-020-06618-2

To date, more than 50 Eimeria spp. have been isolated from marsupials of the family Macropodidae. Although 18 species of Eimeria have been previously detected from multiple animal species belonging to the genus Macropus of the family, limited genetic analyses of the parasites are available, and their pathogenicity remains unclear. Here, we report the isolation of Eimeria spp. from a zoo specimen of red-necked wallaby (Macropodidae; Macropus rufogriseus). Specifically, two distinct types of Eimeria oocysts were recovered, one from the feces before treatment with an anthelmintic and the second from the intestinal contents after death of the animal. The oocysts obtained from the two sources were morphologically identified as E. hestermani and E. prionotemni, respectively. We successfully determined partial gene sequences from the two isolates, including segments of the 18S rRNA genes, and for the first time have used phylogenetic analyses of these sequences to assign the species to distinct clades. In combination with further genetic data, these results are expected to help elucidate the pathogenicity and host ranges of Eimeria spp. within the respective family and genus.

Matched MeSH terms: Phylogeny
Characterization of Aquimarina hainanensis isolated from diseased mud crab Scylla serrata larvae in a hatchery

Midorikawa Y, Shimizu T, Sanda T, Hamasaki K, Dan S, Lal MTBM, et al.

J Fish Dis, 2020 May;43(5):541-549.
PMID: 32147853 DOI: 10.1111/jfd.13151

Mass mortality due to necrosis signs occurred in hatchery-reared zoea stage larvae of the mud crab Scylla serrata in Okinawa, Japan, and a causative bacterium was isolated. In this study, we identified and characterized the bacterium by genome analysis, biochemical properties and pathogenicity. The bacterium was a Gram-negative, non-motile, long rod, forming yellow colonies on a marine agar plate. It grew at 20-33°C (not at 37°C) and degraded chitin and gelatin. Phylogenetic analysis of the 16S rRNA gene sequence identified the bacterium as Aquimarina hainanensis. Genome sequence data obtained from Illumina MiSeq generated 29 contigs with 3.56 Mbp in total length and a G + C content of 32.5%. The predicted 16 chitinase genes, as putative virulence factors, had certain homologies with those of genus Aquimarina. Experimental infection with the bacterium conducted on larvae of four crustacean species, brine shrimp Artemia franciscana, freshwater shrimp Caridina multidentata, swimming crab Portunus trituberculatus and mud crab S. serrata, revealed that this bacterium was highly virulent to these species. The present study suggests that the bacterium caused mass mortality in mud crab seed production was A. hainanensis and can be widely pathogenic to crustaceans.

Matched MeSH terms: Phylogeny
Fulltext Population structure and genetic diversity of Aedes aegypti and Aedes albopictus in Penang as revealed by mitochondrial DNA cytochrome oxidase I

Md Naim D, Kamal NZM, Mahboob S

Saudi J Biol Sci, 2020 Mar;27(3):953-967.
PMID: 32127775 DOI: 10.1016/j.sjbs.2020.01.021

The population genetics study is crucial as it helps in understanding the epidemiological aspects of dengue and help improving a vector control measures. This research aims to investigate the population genetics structure of two common species of Aedes mosquitoes in Penang; Aedes aegypti and Aedes albopictus using Cytochrome Oxidase I (COI) mitochondrial DNA (mtDNA) marker. Molecular investigations were derived from 440 bp and 418 bp mtDNA COI on 125 and 334 larvae of Aedes aegypti and Aedes albopictus respectively, from 32 locations in Penang. All samples were employed in the BLASTn for species identification. The haplotype diversity, nucleotide diversity, neutrality test and mismatch distribution analysis were conducted in DnaSP version 5.10.1. AMOVA analysis was conducted in ARLEQUIN version 3.5 and the phylogenetic reconstructions based on maximum likelihood (ML) and neighbor-joining (NJ) methods were implemented in MEGA X. The relationships among haplotypes were further tested by creating a minimum spanning tree using Network version 4.6.1. All samples were genetically identified and clustered into six distinct species. Among the species, Ae. albopictus was the most abundant (67.2%), followed by Ae. aegypti (25.2%) and the rest were counted for Culex sp. and Toxorhynchites sp. Both Ae. aegypti and Ae. albopictus show low nucleotide diversity (π) and high haplotype diversity (h), while the neutrality test shows a negative value in most of the population for both species. There are a total of 39 and 64 haplotypes recorded for Ae. aegypti and Ae. albopictus respectively. AMOVA analysis revealed that most of the variation occurred within population for both species. Mismatch distribution analysis showed bimodal characteristic of population differentiation for Ae. aegypti but Ae. albopictus showed unimodal characteristics of population differentiation. Genetic distance based on Tamura-Nei parameter showed low genetic divergent within population and high genetic divergent among population for both species. The maximum likelihood tree showed no obvious pattern of population genetic structure for both Ae. aegypti and Ae. albopictus from Penang and a moderate to high bootstrap values has supported this conclusion. The minimum spanning network for Ae. aegypti and Ae. albopictus showed five and three dominant haplotypes respectively, which indicates a mixture of haplotypes from the regions analysed. This study revealed that there is no population genetic structure exhibited by both Ae. aegypti and Ae. albopictus in Penang. Mutation has occurred rapidly in both species and this will be challenging in controlling the populations. However, further analysis needed to confirm this statement.

Matched MeSH terms: Phylogeny

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