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  1. Fulltext First international external quality assessment scheme of nucleic acid amplification tests for the detection of Schistosoma and soil-transmitted helminths, including Strongyloides: A pilot study
    Cools P, van Lieshout L, Koelewijn R, Addiss D, Ajjampur SSR, Ayana M, et al.
    PLoS Negl Trop Dis, 2020 06;14(6):e0008231.
    PMID: 32544158 DOI: 10.1371/journal.pntd.0008231
    BACKGROUND: Nucleic acid amplification tests (NAATs) are increasingly being used as diagnostic tools for soil-transmitted helminths (STHs; Ascaris lumbricoides, Trichuris trichiura, Necator americanus, Ancylostoma duodenale and A. ceylanicum), Strongyloides stercoralis and Schistosoma in human stool. Currently, there is a large diversity of NAATs being applied, but an external quality assessment scheme (EQAS) for these diagnostics is lacking. An EQAS involves a blinded process where test results reported by a laboratory are compared to those reported by reference or expert laboratories, allowing for an objective assessment of the diagnostic performance of a laboratory. In the current study, we piloted an international EQAS for these helminths (i) to investigate the feasibility of designing and delivering an EQAS; (ii) to assess the diagnostic performance of laboratories; and (iii) to gain insights into the different NAAT protocols used.

    METHODS AND PRINCIPAL FINDINGS: A panel of twelve stool samples and eight DNA samples was validated by six expert laboratories for the presence of six helminths (Ascaris, Trichuris, N. americanus, Ancylostoma, Strongyloides and Schistosoma). Subsequently this panel was sent to 15 globally dispersed laboratories. We found a high degree of diversity among the different DNA extraction and NAAT protocols. Although most laboratories performed well, we could clearly identify the laboratories that were poorly performing.

    CONCLUSIONS/SIGNIFICANCE: We showed the technical feasibility of an international EQAS for the NAAT of STHs, Strongyloides and Schistosoma. In addition, we documented that there are clear benefits for participating laboratories, as they can confirm and/or improve the diagnostic performance of their NAATs. Further research should aim to identify factors that explain poor performance of NAATs.

  2. Defining and supporting a professional role for pharmacists associated with traditional and complementary medicines: a cross-country survey of pharmacists
    Harnett JE, Desselle SP, Fernandes MB, Yao D, Modun D, Hallit S, et al.
    Front Pharmacol, 2023;14:1215475.
    PMID: 37654614 DOI: 10.3389/fphar.2023.1215475
    Introduction: An estimated 80% of the world's population use traditional and complementary medicine (T&CM) products as part of their healthcare, with many accessed through pharmacy. This cross-cultural study posed a set of professional practice responsibilities and actions to pharmacists related to T&CM products, with a view toward developing consensus, safeguarding, and promoting the health of the public. Methods: Data were collected from 2,810 pharmacists across nine countries during 2022 via a cross-sectional online survey reported in accordance with the guidelines of STrengthening the Reporting of OBservational studies in Epidemiology (STROBE) and the Checklist for Reporting Results of Internet E-Surveys (CHERRIES). Results: Of the 2,810 participants from nine countries, 2,341 completed all sections of the survey. Of these, most agreed (69%) that T&CM product use was common in the community they served, but most did not have adequate training to support consumer needs. Over 75% acknowledged that there were known and unknown safety risks associated with T&CM use. Of 18 professional responsibilities posed, 92% agreed that pharmacists should be able to inform consumers about potential risks, including T&CM side effects and drug-herb interactions. The provision of accurate scientific information on the effectiveness of T&CM products, skills to guide consumers in making informed decisions, and communication with other healthcare professionals to support appropriate and safe T&CM product use were all ranked with high levels of agreement. In order to effectively fulfill these responsibilities, pharmacists agreed that regulatory reforms, development of T&CM education and training, and access to quality products supported by high-quality evidence were needed. Conclusion: General agreement from across nine countries on eighteen professional responsibilities and several stakeholder actions serve as a foundation for the discussion and development of international T&CM guidelines for pharmacists.
  3. Fulltext Research on cancer diagnosis in Malaysia: current status
    Looi LM, Zubaidah Z, Cheah PL, Cheong SK, Gudum HR, Iekhsan O, et al.
    Malays J Pathol, 2004 Jun;26(1):13-27.
    PMID: 16190103
    Cancer is a major morbidity and mortality concern in Malaysia. Based on National Cancer Registry data, the Malaysian population is estimated to bear a cancer burden of about 40,000 new cases per year, and a cumulative lifetime risk of about 1:4. Cancer research in Malaysia has to consider needs relevant to our population, and resources constraints. Hence, funding bodies prioritise cancers of high prevalence, unique to our community and posing specific clinical problems. Cancer diagnosis is crucial to cancer management. While cancer diagnosis research largely aims at improvements in diagnostic information towards more appropriate therapy, it also impacts upon policy development and other areas of cancer management. The scope of cancer diagnosis upon which this paper is based, and their possible impact on other R&D areas, has been broadly categorized into: (1) identification of aetiological agents and their linkages to the development of precancer and cancer (impact on policy development, cancer prevention and treatment), (2) cancer biology and pathogenesis (impact on cancer prevention, treatment strategies and product development), (3) improvements in accuracy, sensitivity and specificity in cancer detection, monitoring and classification (impact on technology development) and (4) prognostic and predictive parameters (impact on treatment strategies). This paper is based on data collected by the Working Group on Cancer Diagnosis Research for the First National Conference on Cancer Research Coordination in April 2004. Data was collated from the databases of Institutions/Universities where the authors are employed, the Ministry of Science, Technology and Innovation (MOSTI) and targeted survey feedback from key cancer researchers. Under the 7th Malaysia Plan, 76 cancer projects were funded through the Intensified Research in Priority Areas (IRPA) scheme of MOSTI, amounting to almost RM15 million of grant money. 47(61.8%) of these projects were substantially in cancer diagnosis, accounting for 65.6% (RM 9.7 million) of cancer project funds. The 8th Malaysia Plan saw a change in research strategy. The IRPA agency fielded several top-down projects which encouraged a multicentre and multidisciplinary approach. This resulted in larger funding per project i.e. RM32 million for 49 projects. There was also a surge of interest in drug development and natural products. Because of this shift in direction, cancer diagnosis projects constituted only 51% of IRPA-funded cancer projects. Nonetheless funding for cancer diagnosis research has exceeded that of the 7th Malaysia Plan, being RM12.5 million by March 2004. The majority of such research is carried out at the Universities, engaging a large number of young scientists and postgraduate students (51 MSc and 21 PhD). A lot of research findings presented at scientific meetings have not yet been published and there is a glaring shortage of patents and commercialization of research findings (such as creation of test kits). Because diagnosis is very much a part of clinical practice, many researchers felt satisfied and confident that their work will be translated into practice and will significantly improve diagnostic services in Malaysia. National guidelines and consensus development on at least three malignancies i.e. breast cancer, oral cancer and lymphoma, have substantial basis in local R&D work. Problems encountered in research included (1) insufficient funding to realize research objectives, (2) lack of local expertise (most research assistants are inexperienced BSc graduates with no or minimal research experience), (3) inadequate technical support from vendors during equipment failure, (4) inexperienced Institutional development units to assist in product development, (5) lack of venture capital for commercialization of findings, and (6) inadequate incentives to undertake research. Researchers pointed out that plans to promote research should include the establishment of (1) regional and national cancer tissue banks, (2) a National Cancer Research Institute, (3) a dedicated cancer research fund, (4) a registry of cancer researchers, (5) national research coordinators, (6) improved coverage by the National Cancer Registry, (7) more international collaboration, (8) a better career structure for researchers, (9) improved Institutional support for product realization, and (10) better recognition for cancer researchers.
  4. Determining the Dietary Preferences of Wild Asian Elephants (Elephas maximus) in Taman Negara National Park, Malaysia Based on Sex and Age using trnL DNA Metabarcoding Analysis
    Abdullah-Fauzi NAF, Karuppannan KV, Mohd-Radzi NHS, Gani M, Mohd-Ridwan AR, Othman N, et al.
    Zool Stud, 2022;61:e60.
    PMID: 37007822 DOI: 10.6620/ZS.2022.61-60
    The world's largest terrestrial mammal, Asian elephants, are known to have enormous feeding needs. Several factors such as season, sex, age, and daily activities influence the amount of food required by an individual. Generally, captive elephants have a limited choice of food on a daily basis compared with that of elephants in the wild. Elephants in captivity are fed according to a prepared feeding schedule, whereas wild elephants are free to choose the type of plants that they consume in their natural habitat. In the past, ecological observations have been widely used to determine the diet of wild elephants. However, the molecular approach has never been carried out. In the present study, we aimed to; 1) identify the plant diet of wild Asian elephants in Taman Negara National Park (TNNP) according to their sex and age using high-throughput DNA metabarcoding; and 2) determine the dietary formulation of captive elephants based on the generated plant metabarcoding database. DNA was extracted from 24 individual fecal samples collected using noninvasive sampling techniques from TNNP and the National Elephant Conservation Centre (NECC) Kuala Gandah. Seven pooled samples from male adult, female adult, male subadult, female subadult, male juvenile, female juvenile, and captive elephants were amplified and sequenced targeting the trnL region (50-150 base pairs). The CLC Genomic Workbench and PAST 4.02 software were used for data analysis. In total, 24 orders, 41 families, 233 genera, and 306 species of plants were successfully detected in the diet of the Asian elephants. The most abundant plant genera consumed were Sporobolus (21.88%), Musa (21.48%), and Ficus (10.80%). Plant variation was lower in samples from male elephants than in those from female elephants. The plant species identified were correlated with the nutrient benefits required by elephants. Adults and subadults consumed more plant species than were consumed by juvenile elephants. However, there was no significant difference between ages and sexes. The findings of this study can be used as guidance by the Department of Wildlife and National Parks for the management of captive elephants, especially in NECC Kuala Gandah.
  5. Fulltext Microbial Diversity in Decaying Oil Palm Empty Fruit Bunches (OPEFB) and Isolation of Lignin-degrading Bacteria from a Tropical Environment
    Tahir AA, Mohd Barnoh NF, Yusof N, Mohd Said NN, Utsumi M, Yen AM, et al.
    Microbes Environ, 2019 Jun 27;34(2):161-168.
    PMID: 31019143 DOI: 10.1264/jsme2.ME18117
    Oil palm empty fruit bunches (OPEFB) are the most abundant, inexpensive, and environmentally friendly lignocellulosic biomass in Malaysia. Investigations on the microbial diversity of decaying OPEFB may reveal microbes with complex enzymes that have the potential to enhance the conversion of lignocellulose into second-generation biofuels as well as the production of other value-added products. In the present study, fungal and bacterial diversities in decaying OPEFB were identified using Illumina MiSeq sequencing of the V3 region of the 16S rRNA gene and V4 region of the 18S rRNA gene. Fungal diversity in decaying OPEFB was dominated by the phylum Ascomycota (14.43%), while most of the bacterial sequences retrieved belonged to Proteobacteria (76.71%). Three bacterial strains isolated from decaying OPEFB, designated as S18, S20, and S36, appeared to grow with extracted OPEFB-lignin and Kraft lignin (KL) as the sole carbon source. 16S rRNA gene sequencing identified the 3 isolates as Paenibacillus sp.. The molecular weight distribution of KL before and after degradation showed significant depolymerization when treated with bacterial strains S18, S20, and S36. The presence of low-molecular-weight lignin-related compounds, such as vanillin and 2-methoxyphenol derivatives, which were detected by a GC-MS analysis, confirmed the KL-degrading activities of isolated Paenibacillus strains.
  6. Testing comparison models of DASS-12 and its reliability among adolescents in Malaysia
    Osman ZJ, Mukhtar F, Hashim HA, Abdul Latiff L, Mohd Sidik S, Awang H, et al.
    Compr Psychiatry, 2014 Oct;55(7):1720-5.
    PMID: 24952938 DOI: 10.1016/j.comppsych.2014.04.011
    OBJECTIVE: The 21-item Depression, Anxiety and Stress Scale (DASS-21) is frequently used in non-clinical research to measure mental health factors among adults. However, previous studies have concluded that the 21 items are not stable for utilization among the adolescent population. Thus, the aims of this study are to examine the structure of the factors and to report on the reliability of the refined version of the DASS that consists of 12 items.
    METHOD: A total of 2850 students (aged 13 to 17 years old) from three major ethnic in Malaysia completed the DASS-21. The study was conducted at 10 randomly selected secondary schools in the northern state of Peninsular Malaysia. The study population comprised secondary school students (Forms 1, 2 and 4) from the selected schools.
    RESULTS: Based on the results of the EFA stage, 12 items were included in a final CFA to test the fit of the model. Using maximum likelihood procedures to estimate the model, the selected fit indices indicated a close model fit (χ(2)=132.94, df=57, p=.000; CFI=.96; RMR=.02; RMSEA=.04). Moreover, significant loadings of all the unstandardized regression weights implied an acceptable convergent validity. Besides the convergent validity of the item, a discriminant validity of the subscales was also evident from the moderate latent factor inter-correlations, which ranged from .62 to .75. The subscale reliability was further estimated using Cronbach's alpha and the adequate reliability of the subscales was obtained (Total=76; Depression=.68; Anxiety=.53; Stress=.52).
    CONCLUSION: The new version of the 12-item DASS for adolescents in Malaysia (DASS-12) is reliable and has a stable factor structure, and thus it is a useful instrument for distinguishing between depression, anxiety and stress.
  7. Fulltext Molecular testing for advanced non-small cell lung cancer in Malaysia: Consensus statement from the College of Pathologists, Academy of Medicine Malaysia, the Malaysian Thoracic Society, and the Malaysian Oncological Society
    Rajadurai P, Cheah PL, How SH, Liam CK, Annuar MAA, Omar N, et al.
    Lung Cancer, 2019 10;136:65-73.
    PMID: 31446227 DOI: 10.1016/j.lungcan.2019.08.005
    In the recent years, increased understanding of the molecular profiles of non-small cell lung cancer (NSCLC) has allowed for targeted treatment of actionable genetic mutations. The management of NSCLC now requires multiple molecular tests to guide the treatment strategy. In the light of this, there is a need to establish a molecular testing consensus statement for advanced NSCLC patients in Malaysia. This Malaysian consensus statement was developed by a panel of experts, chaired by a pathologist and composed of three other pathologists, four respiratory physicians and three oncologists. It reflects currently available scientific data and adaptations of recommendations from international guidelines to the local landscape. Expert recommendations on different aspects of molecular testing agreed upon by the panel are provided as structured discussions. These recommendations address the appropriate patients and samples to be tested, as well as when and how these tests should be performed. The algorithms for molecular testing in metastatic NSCLC, in the first line setting and upon disease progression beyond first line therapy, were developed.
  8. Fulltext Draft Genome Sequence of the Prazosin-Degrading Bacillus sp. Strain PR5, Isolated from a River Receiving Hospital and Urban Wastewater in Malaysia
    Ahmad Sabri NS, Mohd Mohsi NF, Apandi A, Yusof N, Megat Mohd Noor MJ, Md Akhir FN, et al.
    Microbiol Resour Announc, 2021 Mar 18;10(11).
    PMID: 33737348 DOI: 10.1128/MRA.00025-21
    We report the complete genome sequence of Bacillus sp. strain PR5, isolated from a river receiving hospital and urban wastewater in Malaysia, which demonstrated a high capability for degrading prazosin. This genome sequence of 4,525,264 bp exhibited 41.5% GC content, 4,402 coding sequences, and 32 RNAs.
  9. Fulltext Complete Genome Sequence of Lignin-Degrading Streptomyces sp. Strain S6, Isolated from an Oil Palm Plantation in Malaysia
    Yusof N, Abdullah Tahir A, Riyadi FA, Ahmad Sabri NS, Md Akhir FN, Othman N, et al.
    Microbiol Resour Announc, 2020 Jan 30;9(5).
    PMID: 32001560 DOI: 10.1128/MRA.01332-19
    Streptomyces spp. are bacteria that are responsible for the degradation of aromatic compounds and produce secondary metabolites. Here, we present a complete genome sequence of Streptomyces sp. strain S6, which was isolated from an oil palm plantation, with a 7.8-Mbp liner chromosome, a GC content of 72%, and 4,266 coding sequences.
  10. High incidence of Plasmodium knowlesi malaria compared to other human malaria species in several hospitals in Malaysia
    Lai MY, Rafieqin N, Lee PYL, Amir Rawa MS, Dzul S, Yahaya N, et al.
    Trop Biomed, 2021 Sep 01;38(3):248-253.
    PMID: 34362867 DOI: 10.47665/tb.38.3.065
    Through the regional control programme, Malaysia has been successfully reducing the incidence of Plasmodium falciparum and Plasmodium vivax infections. However, the incidence of zoonotic malaria Plasmodium knowlesi infection is increasing and now has been the major cause of malaria in Malaysia especially Malaysian Borneo. The emergence of knowlesi infection has threatened the malaria elimination programme which the government aims to reduce the overall malaria infections by 2020. Unlike other benign human Plasmodium spp., P. knowlesi can cause fatal infections. The aim of this study was to determine the incidence and distribution of five human malaria parasites including P. knowlesi in Peninsular Malaysia and Malaysian Borneo. A total of 112 blood samples were collected from seven states and district hospitals in Peninsular Malaysia and Malaysian Borneo from year 2015 to 2016. The samples were examined by microscopy and further confirmed by nested PCR assay targeting 18S rRNA gene of Plasmodium spp. Following the nested PCR assays, a total of 54 (48.2%) samples were positive for P. knowlesi infections, 12 (10.7%) cases were positive for P. vivax infections, followed by 7 (6.3%) cases of P. falciparum and 4 (3.5%) cases of P. malariae. There were 3 cases (2.7%) of mixed infections (P. knowlesi/P. vivax). However, no cases were identified as P. ovale. A total of 32 (28.6%) cases were found as negative infections. LoopMediated Isothermal Amplification Assay (LAMP) was performed to confirm inconclusive results produced by microscopy and nested PCR. P. knowlesi showed the highest prevalence in Sarawak (n= 30), Sabah (n=13), Pulau Pinang (n=5) and Pahang (n=6). PCR and LAMP was not able to detect a large number of microscopy positive samples due to DNA degradation during storage and shipping. Among all the states involved in this study, the highest prevalence of P. knowlesi infection was found in Sabah and Sarawak.
  11. Fulltext Effects of gamma irradiation on tropomyosin allergen, proximate composition and mineral elements in giant freshwater prawn (Macrobrachium rosenbergii)
    Muanghorn W, Konsue N, Sham H, Othman Z, Mohamed F, Mohd Noor N, et al.
    J Food Sci Technol, 2018 May;55(5):1960-1965.
    PMID: 29666550 DOI: 10.1007/s13197-018-3104-3
    Effects of food irradiation on allergen and nutritional composition of giant freshwater prawn are not well documented. Thus, this study aimed to investigate the effects of gamma irradiation on tropomyosin allergen, proximate composition, and mineral elements in Macrobrachium rosenbergii. In this study, prawn was peeled, cut into small pieces, vacuum packaged and gamma irradiated at 0, 5, 7, 10 and 15 kGy with a dose rate of 0.5 kGy/h using cobalt-60 as the source, subsequently determined the level of tropomyosin, proximate composition and mineral elements respectively. The results showed that band density of tropomyosin irradiated at 10 and 15 kGy is markedly decreased. Proximate analysis revealed that moisture, protein, and carbohydrate content were significantly different as compared with non-irradiated prawn. Meanwhile, gamma irradiated M. rosenbergii at 15 kGy was observed to be significantly higher in nickel and zinc than the non-irradiated prawn. The findings provide a new information that food irradiation may affect the tropomyosin allergen, proximate composition and mineral elements of the prawn.
  12. Fulltext Biocide susceptibilities and biofilm-forming capacities of Acinetobacter baumannii clinical isolates from Malaysia
    Nor A'shimi MH, Alattraqchi AG, Mohd Rani F, A Rahman NI, Ismail S, Abdullah FH, et al.
    J Infect Dev Ctries, 2019 07 31;13(7):626-633.
    PMID: 32065820 DOI: 10.3855/jidc.11455
    INTRODUCTION: Acinetobacter baumannii is a Gram-negative nosocomial pathogen that has the capacity to develop resistance to all classes of antimicrobial compounds. However, very little is known regarding its susceptibility to biocides (antiseptics and disinfectants) and capacity to form biofilms, particularly for Malaysian isolates.

    AIM: To determine the susceptibility of A. baumannii isolates to commonly-used biocides, investigate their biofilm-forming capacities and the prevalence of biocide resistance and biofilm-associated genes.

    METHODOLOGY: . The minimum inhibitory concentration (MIC) values of 100 A. baumannii hospital isolates from Terengganu, Malaysia, towards the biocides benzalkonium chloride (BZK), benzethonium chloride (BZT) and chlorhexidine digluconate (CLX), were determined by broth microdilution. The isolates were also examined for their ability to form biofilms in 96-well microplates. The prevalence of biocide resistance genes qacA, qacE and qacDE1 and the biofilm-associated genes bap and abaI were determined by polymerase chain reaction (PCR).

    RESULTS: Majority of the A. baumannii isolates (43%) showed higher MIC values (> 50 µg/mL) for CLX than for BZK (5% for MIC > 50 µg/mL) and BZT (9% for MIC > 50 µg/mL). The qacDE1 gene was predominant (63%) followed by qacE (28%) whereas no isolate was found harbouring qacA. All isolates were positive for the bap and abaI genes although the biofilm-forming capacity varied among the isolates.

    CONCLUSION: The Terengganu A. baumannii isolates showed higher prevalence of qacDE1 compared to qacE although no correlation was found with the biocides' MIC values. No correlation was also observed between the isolates' biofilm-forming capacity and the MIC values for the biocides.

  13. Fulltext Data on First Record of Brown Morph Banded Langur (Presbytis femoralis), Leucistic Dusky Leaf Monkey (Trachypithecus obscurus) in Malaysia and Review of Morph Diversity in Langur (Colobinae)
    Najmuddin MF, Haris H, Othman N, Zahari F, Mohd-Ridwan AR, Md-Zain BM, et al.
    Data Brief, 2020 Aug;31:105727.
    PMID: 32548216 DOI: 10.1016/j.dib.2020.105727
    Morphism refer to polymorphic species, in which multiple colour variants coexist within a population. Morphism in primates is common and langurs also exhibit certain characteristics of morphism, such as conspicuous natal coats. Banded langurs (Presbytis femoralis) and dusky leaf monkey (Trachypithecus obscurus) exhibits the same characteristics of conspicuous natal coats, but these coats are only limited to infants and changed when they reached adulthood. This article reports the first discovery of rare brown morph of two adult male banded langurs and one leucistic adult female dusky leaf monkey in Malaysia. We also conducted a systematic literature search to review the diversity of morphism in leaf monkey globally.
  14. Fulltext Adsorption of Zn2+ from Synthetic Wastewater Using Dried Watermelon Rind (D-WMR): An Overview of Nonlinear and Linear Regression and Error Analysis
    Altowayti WAH, Othman N, Al-Gheethi A, Dzahir NHBM, Asharuddin SM, Alshalif AF, et al.
    Molecules, 2021 Oct 13;26(20).
    PMID: 34684757 DOI: 10.3390/molecules26206176
    Sustainable wastewater treatment is one of the biggest issues of the 21st century. Metals such as Zn2+ have been released into the environment due to rapid industrial development. In this study, dried watermelon rind (D-WMR) is used as a low-cost adsorption material to assess natural adsorbents' ability to remove Zn2+ from synthetic wastewater. D-WMR was characterized using scanning electron microscope (SEM) and X-ray fluorescence (XRF). According to the results of the analysis, the D-WMR has two colours, white and black, and a significant concentration of mesoporous silica (83.70%). Moreover, after three hours of contact time in a synthetic solution with 400 mg/L Zn2+ concentration at pH 8 and 30 to 40 °C, the highest adsorption capacity of Zn2+ onto 1.5 g D-WMR adsorbent dose with 150 μm particle size was 25 mg/g. The experimental equilibrium data of Zn2+ onto D-WMR was utilized to compare nonlinear and linear isotherm and kinetics models for parameter determination. The best models for fitting equilibrium data were nonlinear Langmuir and pseudo-second models with lower error functions. Consequently, the potential use of D-WMR as a natural adsorbent for Zn2+ removal was highlighted, and error analysis indicated that nonlinear models best explain the adsorption data.
  15. Fulltext Limitation of nutrients stimulates musty odor production by Streptomyces sp. isolated from a tropical environment
    Shudirman S, Abang Kassim A, Shamsol Anuar NS, Utsumi M, Shimizu K, Muhammad Yuzir MA, et al.
    J Gen Appl Microbiol, 2021 Jul 31;67(3):92-99.
    PMID: 33642451 DOI: 10.2323/jgam.2020.08.001
    Musty odor production by actinomycetes is usually related to the presence of geosmin and 2-methylisoborneol (2-MIB), which are synthesized by enzymes encoded by the geoA and tpc genes, respectively. Streptomyces spp. strain S10, which was isolated from a water reservoir in Malaysia, has the ability to produce geosmin when cultivated in a basal salt (BS) solid medium, but no 2-MIB production occurred during growth in BS medium. Strain S10 could produce higher levels of geosmin when the phosphate concentration was limited to 0.05 mg/L, with a yield of 17.53 ± 3.12 ✕ 105 ng/L, compared with growth in BS medium. Interestingly, 2-MIB production was suddenly detected when the nitrate concentration was limited to 1.0 mg/L, with a yield of 1.4 ± 0.11 ✕ 105 ng/L. Therefore, it was concluded that phosphate- and nitrate-limiting conditions could induce the initial production of geosmin and 2-MIB by strain S10. Furthermore, a positive amplicon of geoA was detected in strain S10, but no tpc amplicon was detected by PCR analysis. Draft genome sequence analysis showed that one open reading frame (ORF) contained a conserved motif of geosmin synthase with 95% identity with geoA in Streptomyces coelicolor A3 (2). In the case of the tpc genes, it was found that one ORF showed 23% identity to the known tpc gene in S. coelicolor A3(2), but strain S10 lacked one motif in the N-terminus.
  16. Determining the diet of wild Asian elephants (Elephasmaximus) at human-elephant conflict areas in Peninsular Malaysia using DNA metabarcoding
    Mohd-Radzi NHS, Karuppannan KV, Abdullah-Fauzi NAF, Mohd-Ridwan AR, Othman N, Muhammad Abu Bakar AL, et al.
    Biodivers Data J, 2022;10:e89752.
    PMID: 36761586 DOI: 10.3897/BDJ.10.e89752
    Human-elephant conflict (HEC) contributes to the increasing death of Asian elephants due to road accidents, retaliatory killings and fatal infections from being trapped in snares. Understanding the diet of elephants throughout Peninsular Malaysia remains crucial to improve their habitat quality and reduce scenarios of HEC. DNA metabarcoding allows investigating the diet of animals without direct observation, especially in risky conflict areas. The aim of this study was to determine: i) the diet of wild Asian elephants from HEC areas in Peninsular Malaysia using DNA metabarcoding and ii) the influence of distinct environmental parameters at HEC locations on their feeding patterns. DNA was extracted from 39 faecal samples and pooled into 12 groups representing the different sample locations: Kuala Koh, Kenyir, Ulu Muda, Sira Batu, Kupang-Grik, Bumbun Tahan, Belum-Temengor, Grik, Kampung Pagi, Kampung Kuala Balah, Aring 10 and the National Elephant Conservation Centre, which served as a positive control for this study. DNA amplification and sequencing targeted the ribulose-bisphosphate carboxylase gene using the next-generation sequencing Illumina iSeq100 platform. Overall, we identified 35 orders, 88 families, 196 genera and 237 species of plants in the diet of the Asian elephants at HEC hotspots. Ficus (Moraceae), Curcuma (Zingiberaceae), Phoenix (Arecaceae), Maackia (Fabaceae), Garcinia (Clusiaceae) and Dichapetalum (Dichapetalaceae) were the highly abundant dietary plants. The plants successfully identified in this study could be used by the Department of Wildlife and National Parks (PERHILITAN) to create buffer zones by planting the recommended dietary plants around HEC locations and trails of elephants within Central Forest Spine (CFS) landscape.
  17. First documentation on herpetofauna diversity in Gunung Belumut Amenity Forest, Peninsular Malaysia: Implications for conservation in an Environmentally Sensitive Area (ESA)
    Ramli FF, Munian K, Mahyudin NAA, Othman N, Haris H, Abdullah-Fauzi NAF, et al.
    Biodivers Data J, 2024;12:e108476.
    PMID: 38235165 DOI: 10.3897/BDJ.12.e108476
    Malaysia is blessed with lush tropical rainforests that harbour an exceptional diversity of amphibians and reptiles. However, compared to other animal groups, amphibians and reptiles have received limited attention in research, despite their ecological significance. With amphibians and reptile species having been declining rapidly due to anthropogenic activities, there is a pressing need to conserve these species and their habitats. Environmentally Sensitive Areas (ESAs) are designated regions that are beneficial due to their critical role in providing essential ecosystem services and serving as repositories of biodiversity. Nonetheless, the classification of ESAs in Malaysia lacks biological elements and only focuses on physical attributes. To enhance the current ESA classification framework by integrating biological components, there is an urgent need to obtain information on diversity and habitat in Malaysia. Therefore, the objectives of this study were twofold: to determine the diversity of amphibians and reptiles in Gunung Belumut Amenity Forest and to conduct a comparative analysis between the herpetofauna assemblages in Gunung Belumut with other forest reserves in Peninsular Malaysia. The survey was carried out between March and June 2022, with additional sampling conducted in February 2023. The Visual Encounter Survey (VES) and pitfall trap methods were employed to survey the herpetofauna species, focusing on both aquatic and terrestrial habitats within the study area. A total of 210 individuals representing 38 species of herpetofauna were recorded, comprising 18 amphibian and 20 reptile species. Amongst the observed species, Limnonectesblythii was the most frequently encountered amphibian, with 59 individuals observed, while the dominant reptile species was Cyrtodactylusconsobrinus, represented by eight individuals. This pioneering study serves as a vital baseline documentation of the amphibian and reptile assemblages in Gunung Belumut Amenity Forest. It provides valuable information for identifying extant herpetofauna species, including those of potential conservation concern or rarity. These findings contribute to ongoing conservation efforts dedicated to the preservation of herpetofauna within the region. By understanding the diversity and distribution patterns of amphibians and reptiles in Gunung Belumut, effective conservation strategies can be developed to protect these species and their habitats.
  18. Fulltext Predominance and emergence of clones of hospital-acquired methicillin-resistant Staphylococcus aureus in Malaysia
    Ghaznavi-Rad E, Nor Shamsudin M, Sekawi Z, Khoon LY, Aziz MN, Hamat RA, et al.
    J Clin Microbiol, 2010 Mar;48(3):867-72.
    PMID: 20089756 DOI: 10.1128/JCM.01112-09
    We define the epidemiology of predominant and sporadic methicillin-resistant Staphylococcus aureus (MRSA) strains in a central teaching and referral hospital in Kuala Lumpur, Malaysia. This is done on the basis of spa sequencing, multilocus sequence typing (MLST), staphylococcal cassette chromosome mec (SCCmec) typing, and virulence gene profiling. During the period of study, the MRSA prevalence was 44.1%, and 389 MRSA strains were included. The prevalence of MRSA was found to be significantly higher in the patients of Indian ethnicity (P < 0.001). The majority (92.5%) of the isolates belonged to ST-239, spa type t037, and possessed the type III or IIIA SCCmec. The arginine catabolic mobile element (ACME) arcA gene was detected in three (1.05%) ST-239 isolates. We report the first identification of ACME arcA gene-positive ST-239. Apart from this predominant clone, six (1.5%) isolates of ST-22, with two related spa types (t032 and t4184) and a singleton (t3213), carrying type IVh SCCmec, were detected for the first time in Asia. A limited number of community-acquired (CA) MRSA strains were also detected. These included ST-188/t189 (2.1%), ST-1/t127 (2.3%), and ST-7/t091 (1%). Panton-Valentin leukocidin (PVL) was detected in all ST-1 and ST-188 strains and in 0.7% of the ST-239 isolates. The majority of the isolates carried agr I, except that ST-1 strains were agr III positive. Virulence genes seg and sei were seen only among ST-22 isolates. In conclusion, current results revealed the predominance of ST-239-SCCmec III/IIIA and the penetration of ST-22 with different virulence gene profiles. The emergence in Malaysia of novel clones of known epidemic and pathogenic potential should be taken seriously.
  19. The cadmium tolerance and bioaccumulation mechanism of Tetratostichococcus sp. P1: insight from transcriptomics analysis
    Sahabudin E, Kubo S, Yuzir MAM, Othman N, Nadia Md Akhir F, Suzuki K, et al.
    Bioengineered, 2024 Dec;15(1):2314888.
    PMID: 38375815 DOI: 10.1080/21655979.2024.2314888
    Cadmium (Cd) has become a severe issue in relatively low concentration and attracts expert attention due to its toxicity, accumulation, and biomagnification in living organisms. Cd does not have a biological role and causes serious health issues. Therefore, Cd pollutants should be reduced and removed from the environment. Microalgae have great potential for Cd absorption for waste treatment since they are more environmentally friendly than existing treatment methods and have strong metal sorption selectivity. This study evaluated the tolerance and ability of the microalga Tetratostichococcus sp. P1 to remove Cd ions under acidic conditions and reveal mechanisms based on transcriptomics analysis. The results showed that Tetratostichococcus sp. P1 had a high Cd tolerance that survived under the presence of Cd up to 100 µM, and IC50, the half-maximal inhibitory concentration value, was 57.0 μM, calculated from the change in growth rate based on the chlorophyll content. Long-term Cd exposure affected the algal morphology and photosynthetic pigments of the alga. Tetratostichococcus sp. P1 removed Cd with a maximum uptake of 1.55 mg g-1 dry weight. Transcriptomic analysis revealed the upregulation of the expression of genes related to metal binding, such as metallothionein. Group A, Group B transporters and glutathione, were also found upregulated. While the downregulation of the genes were related to photosynthesis, mitochondria electron transport, ABC-2 transporter, polysaccharide metabolic process, and cell division. This research is the first study on heavy metal bioremediation using Tetratostichococcus sp. P1 and provides a new potential microalga strain for heavy metal removal in wastewater.[Figure: see text]Abbreviations:BP: Biological process; bZIP: Basic Leucine Zipper; CC: Cellular component; ccc1: Ca (II)-sensitive cross complementary 1; Cd: Cadmium; CDF: Cation diffusion facilitator; Chl: Chlorophyll; CTR: Cu TRansporter families; DAGs: Directed acyclic graphs; DEGs: Differentially expressed genes; DVR: Divinyl chlorophyllide, an 8-vinyl-reductase; FPN: FerroportinN; FTIR: Fourier transform infrared; FTR: Fe TRansporter; GO: Gene Ontology; IC50: Growth half maximal inhibitory concentration; ICP: Inductively coupled plasma; MF: molecular function; NRAMPs: Natural resistance-associated aacrophage proteins; OD: Optical density; RPKM: Reads Per Kilobase of Exon Per Million Reads Mapped; VIT1: Vacuolar iron transporter 1 families; ZIPs: Zrt-, Irt-like proteins.
  20. Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool
    Munian K, Ramli FF, Othman N, Mahyudin NAA, Sariyati NH, Abdullah-Fauzi NAF, et al.
    Mol Ecol Resour, 2024 May;24(4):e13936.
    PMID: 38419264 DOI: 10.1111/1755-0998.13936
    The approach of combining cost-effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for biodiversity documentation, especially in Malaysia. Given the substantial funding constraints in recent years, especially in relation to the country's biodiversity, many researchers have been limited to conduct restricted research without extended monitoring periods, potentially hindering comprehensive surveys and could compromise the conservation efforts. Therefore, the present study aimed to evaluate the application of eDNA metabarcoding on freshwater fish using short reads generated through nanopore sequencing. This assessment focused on species detection in three selected rivers within the Endau Rompin Landscape in Malaysia. Additionally, the study compared levels of species detection between eDNA metabarcoding and conventional sampling methods, examined the effectiveness of primer choice, and applied both metabarcoding and shotgun sequencing to the eDNA approach. We successfully identified a total of 22 and 71 species with an identification threshold of >97% and >90%, respectively, through the MinION platform. The eDNA metabarcoding approach detected over 13% more freshwater fish species than when the conventional method was used. Notably, the distinction in freshwater fish detection between eDNA primers for 12S rRNA and cytochrome oxidase I was insignificant. The cost for eDNA metabarcoding proved to be more effective compared to conventional sampling with cost reduction at 33.4%. With favourable cost-effectiveness and increased species detection, eDNA metabarcoding could complement existing methods, enhance holistic diversity documentation for targeted habitats and facilitate effective conservation planning.
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