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Development of an algorithm of satellite markers for monitoring chimerism status in post-allogeneic haematopoietic stem cell transplantation patients

Choong SS, Rosmanizam S, Ibrahim K, Gan GG, Ariffin H

Int J Lab Hematol, 2011 Apr;33(2):182-6.
PMID: 20868447 DOI: 10.1111/j.1751-553X.2010.01264.x

Analysis of variable number tandem repeats (VNTRs) by polymerase chain reaction (PCR) is a common method used to predict engraftment status in post-allogeneic haematopoeitic stem cell transplantation (HSCT) patients. Different populations have different copies of repeated DNA sequence and hence, different percentage of informativeness between patient and donor.
Amblyomma cordiferum Neumann, 1899 (Acari: Ixodidae) parasitizing reticulated pythons, Malayopython reticulatus (Schneider, 1801) (Reptilia: Pythonidae) in Peninsular Malaysia

Tan LP, Choong SS, Samsuddin AS, Lee SH

Ticks Tick Borne Dis, 2019 10;10(6):101285.
PMID: 31494069 DOI: 10.1016/j.ttbdis.2019.101285

Two ticks were collected from a reticulated python (Malayopython reticulatus) caught in Tumpat District, Kelantan, Peninsular Malaysia. The ticks were first identified as Ambylomma sp. through morphological comparison with identification keys. Determination of the tick species was made through PCR and sequencing. However, BLAST analysis revealed 85-88% sequence nucleotide identity with Amblyomma nitidum and Amblyomma geoemydae. Additionally, the morphological features of the ticks collected in this study did not match either A. nitidum or A. geoemydae. Further examination of the ticks confirmed the species as Amblyomma cordiferum. This is the first record of A. cordiferum DNA sequence with morphological support of colour illustrations for adult A. cordiferum. This is also the most recent record of this host association in Peninsular Malaysia. Information from this report can serve as a reference for species identification using the described morphology or molecular sequences.
First report of equine Setaria digitata (von Linstow 1906) infestation in Malaysia

Peng TL, Armiladiana MM, Ruhil HH, Maizan M, Choong SS

Vet Parasitol Reg Stud Reports, 2019 08;17:100310.
PMID: 31303218 DOI: 10.1016/j.vprsr.2019.100310

The occurrence of Setaria digitata in a horse is reported for the first time in Malaysia. An 8-year-old Thoroughbred cross mare was referred to the University Veterinary Clinic with the primary complaint of corneal opacity and excessive eye discharge. After initial treatment with Terramycin eye ointment, corneal opacity cleared partially to reveal a moving thread-like cylindrical worm in the anterior chamber of the eye. The parasite was successfully removed surgically, and examination under the light microscope revealed that the isolated worm (length = 45 mm) was a 5th stage larva of S. digitata based on morphological criteria. Confirmation of the species of the worm was through molecular methods. The 12S rRNA gene was PCR-amplified, and the purified amplicon was directly sequenced. Phylogenetic analyses revealed that the isolated roundworm showed 100% sequence similarity with that of S. digitata in NCBI GenBank database (Accession no.: KY284626.1). This report is the first confirmed case of equine ocular setariasis by S. digitata in Malaysia. The current study provides evidence that S. digitata is an etiological agent of ocular infection and its presence in Malaysia.
Prevalence of parasites in working pig-tailed Macaques (Macaca nemestrina) in Kelantan, Malaysia

Choong SS, Mimi Armiladiana M, Ruhil HH, Peng TL

J Med Primatol, 2019 08;48(4):207-210.
PMID: 31025372 DOI: 10.1111/jmp.12416

BACKGROUND: Coconut is an important commodity in Kelantan, and pig-tailed macaques (Macaca nemestrina) have been traditionally used for coconut-plucking for over a century. Most of these animals were sourced from the wild population, and the parasitic status of these macaques is unknown, plus the impacts caused by these parasites are usually underestimated by the owners.
METHODS: A total of 30 macaques were sampled for blood, faeces and hair plucks to detect parasite.
RESULTS: Out of 21 faecal samples examined, 11 (52%) were determined positive for one or more gastrointestinal parasites, namely Trichostrongylus spp., Strongyloides spp., Anatrichosoma spp., Capillaria spp., Trichuris spp. and Paramphisotomum spp. Filaria was detected in one (3%) of the blood samples. For ectoparasites, only lice, Pedicinus sp., were found in 9 (30%) macaques.
CONCLUSIONS: It is imperative that the parasitic status of these animals be determined so that necessary actions and preventive measures can be implemented to prevent zoonotic transmissions.
Fulltext GATA1 mutations in a cohort of Malaysian children with Down syndrome-associated myeloid disorder

Lum SH, Choong SS, Krishnan S, Mohamed Z, Ariffin H

Singapore Med J, 2016 Jun;57(6):320-4.
PMID: 27353457 DOI: 10.11622/smedj.2016106

INTRODUCTION: Children with Down syndrome (DS) are at increased risk of developing distinctive clonal myeloid disorders, including transient abnormal myelopoiesis (TAM) and myeloid leukaemia of DS (ML-DS). TAM connotes a spontaneously resolving congenital myeloproliferative state observed in 10%-20% of DS newborns. Following varying intervals of apparent remission, a proportion of children with TAM progress to develop ML-DS in early childhood. Therefore, TAM and ML-DS represent a biological continuum. Both disorders are characterised by recurring truncating somatic mutations of the GATA1 gene, which are considered key pathogenetic events.
METHODS: We herein report, to our knowledge, the first observation on the frequency and nature of GATA1 gene mutations in a cohort of Malaysian children with DS-associated TAM (n = 9) and ML-DS (n = 24) encountered successively over a period of five years at a national referral centre.
RESULTS: Of the 29 patients who underwent GATA1 analysis, GATA1 mutations were observed in 15 (51.7%) patients, including 6 (75.0%) out of 8 patients with TAM, and 9 (42.9%) of 21 patients with ML-DS. All identified mutations were located in exon 2 and the majority were sequence-terminating insertions or deletions (66.7%), including several hitherto unreported mutations (12 out of 15).
CONCLUSION: The low frequency of GATA1 mutations in ML-DS patients is unusual and potentially indicates distinctive genomic events in our patient cohort.
Fulltext Preference and intake frequency of high sodium foods and dishes and their correlations with anthropometric measurements among Malaysian subjects

Choong SS, Balan SN, Chua LS, Say YH

Nutr Res Pract, 2012 Jun;6(3):238-45.
PMID: 22808349 DOI: 10.4162/nrp.2012.6.3.238

This study investigated the preference and intake frequency of a list of 15 commonly available high sodium Malaysian foods/dishes, discretionary salt use, and their possible association with demographics, blood pressures and anthropometric measurements among 300 Malaysian university students (114 males, 186 females; 259 ethnic Chinese, 41 Indians; 220 lean, 80 overweight). French fries and instant soup noodle were found to be the most preferred and most frequently consumed salty food, respectively, while salted fish was least preferred and least frequently consumed. Males had a significantly higher intake frequency of at least 6 of the salty foods, but the preference of most salty foods was not significantly different between genders. Ethnic Chinese significantly preferred more and took more frequently traditional and conventional Malaysian foods like asam laksa (a Malaysian salty-sour-spicy noodle in fish stock), salted biscuits and salted vegetable, while Indians have more affinity and frequency towards eating salty Western foods. Body Mass Index was significantly negatively correlated with the intake frequency of canned/packet soup and salted fish while waist circumference was significantly positively correlated with the preference of instant noodle. Also, an increased preference of potato chips and intake frequency of salted biscuits seemed to lead to a decreased WHR. Other than these, all the other overweight/obesity indicators did not seem to fully correlate with the salty food preference and intake frequency. Nevertheless, the preference and intake frequency of asam laksa seemed to be significant negative predictors for blood pressures. Finally, increased preference and intake frequency of high sodium shrimp paste (belacan)-based foods like asam laksa and belacan fried rice seemed to discourage discretionary salt use. In conclusion, the preference and intake frequency of the high sodium belacan-based dish asam laksa seems to be a good predictor for ethnic difference, discretionary salt use and blood pressures.
Microfluidic chip-based assay for post-hematopoietic stem cell transplantation chimerism monitoring using polymorphic tandem repeat markers

Daud SS, Ibrahim K, Choong SS, Vengidasan L, Chong LA, Ariffin H

Anal Biochem, 2010 Feb 15;397(2):181-5.
PMID: 19822126 DOI: 10.1016/j.ab.2009.10.008

Following hematopoietic stem cell transplantation (HSCT), it is important to determine whether engraftment is successful and to track the dynamic changes of the graft. Tandem repeats such as minisatellites and microsatellites are currently the most established markers for chimerism application. We have developed a reliable method to quantitatively evaluate engraftment status in post-allogeneic HSCT patients using variable number of tandem repeat (VNTR) markers and "lab-on-a-chip" microfluidic electrophoresis technology. Following identification of an informative marker by conventional polymerase chain reaction (PCR), donor chimerism percentage was calculated based on a standard curve generated from artificially mixed patient-donor DNA-specific alleles in serial dilutions. All PCR products were mixed with commercial gel dye and loaded into Agilent DNA 1000 microfluidic LabChips for DNA sizing and quantitation. In 44 patients, separation of pretransplant and donor DNA fragments was resolved clearly and accomplished rapidly within 30min. Chimerism analysis using this platform is able to detect an amount as low as 6.3% donor DNA with acceptable coefficient of variation values. We also demonstrated concordant chimerism analysis findings using both microchip tandem repeats and real-time PCR quantitation of insertion-deletion polymorphisms. This microchip platform obviates the need for fluorescently labeled primers or any post-PCR sample manipulation. Quantitative monitoring of post-HSCT chimerism status using microfluidic electrophoresis is a useful tool for both large- and small-scale post-HSCT chimerism centers.
Presence of SARS-CoV-2-like coronaviruses in bats from east coast Malaysia

Gilbert M, Mohamed M, Choong SS, Baqi A, Kumaran JV, Sani I, et al.

Trop Biomed, 2023 Sep 01;40(3):273-280.
PMID: 37897158 DOI: 10.47665/tb.40.3.001

Most of the public health importance coronaviruses, such as Severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV-2 are likely originated from bats and spread to humans through intermediate hosts; civet cats, dromedary camel and Malayan pangolin, respectively. SARS-CoV-2-like coronaviruses were detected in Thailand, which is neighbouring with Kelantan in East Coast Malaysia. To date, there is no report on the presence of public health concerns (SARS-CoV, SARS-CoV-2 and MERS-CoV) coronaviruses in bats from Malaysia. This study was aimed to elucidate the presence of these coronaviruses in bat samples from East Coast, Malaysia. A total of hundred seventy oropharyngeal swab samples were collected from three states of East Coast Malaysia. Reverse Transcription-Polymerase Chain Reaction (RT-PCR) was conducted based on partial 3' Untranslated region (3'UTR) or ORF10 gene and the products were sequenced. The sequences were compared with all coronavirus sequences from the National Center for Biotechnology Information-GenBank (NCBI-GenBank) using NCBI-Basic Local Alignment Search Tool (NCBI-BLAST) software. A phylogenetic tree was constructed to determine the genetic relationship among the detected coronaviruses with the reference coronaviruses from the NCBI-GenBank. Our results showed that SARSCoV-2-like viruses were present in 3% (5/170) of the bats from East Coast Malaysia that have 98-99% sequence identities and are genetically related to SARS-CoV-2 from humans. This finding indicates the presence of SARS-CoV-2-like viruses in bats from East Coast Malaysia that may become a public health concern in the future.
Childhood adrenocortical carcinoma as a sentinel cancer for detecting families with germline TP53 mutations

Choong SS, Latiff ZA, Mohamed M, Lim LL, Chen KS, Vengidasan L, et al.

Clin Genet, 2012 Dec;82(6):564-8.
PMID: 22233476 DOI: 10.1111/j.1399-0004.2012.01841.x

Li-Fraumeni syndrome (LFS) is a highly penetrant, autosomal dominant disorder where affected individuals carry a 50% risk of developing cancer before 30 years of age. It is most commonly associated with mutations in the tumour suppressor gene, TP53. Adrenocortical carcinoma (ACC) is a very rare paediatric cancer, and up to 80% of affected children are found to carry germline TP53 mutations. Hence, we propose using childhood ACC incidence as selection criteria for referral for TP53 mutation testing, independent of familial cancer history. Under the auspices of the Malaysian Society of Paediatric Haematology-Oncology, four eligible children diagnosed with ACC over a 30-month study period were referred for mutation testing. Three had a germline TP53 mutation. Subsequent TP53 testing in relatives showed two inherited mutations and one de novo mutation. These findings strongly support paediatric ACC as a useful sentinel cancer for initiating a germline TP53/LFS detection programme, particularly in countries where the lack of structured oncogenetic practice precludes the identification of families with LFS features.
Fulltext First case report on the occurrence of Trypanosoma evansi in a Siam B Mare in Kelantan, Malaysia

Mohd Rajdi NZI, Mohamad MA, Tan LP, Choong SS, Reduan MFH, Hamdan RH, et al.

Vet Med Sci, 2021 Mar;7(2):303-309.
PMID: 33161648 DOI: 10.1002/vms3.379

This is the first case report for the positive Trypanosoma evansi incident in Kelantan, Malaysia confirmed through protozoa detection in a Siam B mare. The horse was presented with complaints of lethargy and inappetence and it collapsed on the day of visit. Normal saline and dextrose solution were administered intravenously, while multivitamins and nerve supplements were given intramuscularly to stabilise the horse before further treatment. Haematological findings showed normocytic hypochromic anaemia and are suggestive of regenerative anaemia. Thin blood smear and examination revealed the presence of Trypanosoma sp., and it was confirmed as T. evansi through molecular identification. The horse was found dead 2 days after and post-mortem was conducted. Histopathology revealed that the horse had developed a neurological form of the disease, besides the detection of the protozoa in heart, spleen and kidney tissue. This first positive Surra case in Kelantan, Malaysia, that is bordering Thailand confirms the increasing concern of transboundary infections. In conclusion, Surra is a potential emerging disease and should be considered as differential diagnosis in horses with pale mucous membrane. This condition is particularly imperative in horses found in these regions as Surra is endemic.
Fulltext Antimicrobial Polymers: The Potential Replacement of Existing Antibiotics?

Kamaruzzaman NF, Tan LP, Hamdan RH, Choong SS, Wong WK, Gibson AJ, et al.

Int J Mol Sci, 2019 Jun 04;20(11).
PMID: 31167476 DOI: 10.3390/ijms20112747

Antimicrobial resistance is now considered a major global challenge; compromising medical advancements and our ability to treat infectious disease. Increased antimicrobial resistance has resulted in increased morbidity and mortality due to infectious diseases worldwide. The lack of discovery of novel compounds from natural products or new classes of antimicrobials, encouraged us to recycle discontinued antimicrobials that were previously removed from routine use due to their toxicity, e.g., colistin. Since the discovery of new classes of compounds is extremely expensive and has very little success, one strategy to overcome this issue could be the application of synthetic compounds that possess antimicrobial activities. Polymers with innate antimicrobial properties or that have the ability to be conjugated with other antimicrobial compounds create the possibility for replacement of antimicrobials either for the direct application as medicine or implanted on medical devices to control infection. Here, we provide the latest update on research related to antimicrobial polymers in the context of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) pathogens. We summarise polymer subgroups: compounds containing natural peptides, halogens, phosphor and sulfo derivatives and phenol and benzoic derivatives, organometalic polymers, metal nanoparticles incorporated into polymeric carriers, dendrimers and polymer-based guanidine. We intend to enhance understanding in the field and promote further work on the development of polymer based antimicrobial compounds.
Fulltext Targeting the Bacterial Protective Armour; Challenges and Novel Strategies in the Treatment of Microbial Biofilm

Kamaruzzaman NF, Tan LP, Mat Yazid KA, Saeed SI, Hamdan RH, Choong SS, et al.

Materials (Basel), 2018 Sep 13;11(9).
PMID: 30217006 DOI: 10.3390/ma11091705

Infectious disease caused by pathogenic bacteria continues to be the primary challenge to humanity. Antimicrobial resistance and microbial biofilm formation in part, lead to treatment failures. The formation of biofilms by nosocomial pathogens such as Staphylococcus aureus (S. aureus), Pseudomonas aeruginosa (P. aeruginosa), and Klebsiella pneumoniae (K. pneumoniae) on medical devices and on the surfaces of infected sites bring additional hurdles to existing therapies. In this review, we discuss the challenges encountered by conventional treatment strategies in the clinic. We also provide updates on current on-going research related to the development of novel anti-biofilm technologies. We intend for this review to provide understanding to readers on the current problem in health-care settings and propose new ideas for new intervention strategies to reduce the burden related to microbial infections.
Fulltext Whole-genome sequencing analysis of phenotypic heterogeneity and anticipation in Li-Fraumeni cancer predisposition syndrome

Ariffin H, Hainaut P, Puzio-Kuter A, Choong SS, Chan AS, Tolkunov D, et al.

Proc Natl Acad Sci U S A, 2014 Oct 28;111(43):15497-501.
PMID: 25313051 DOI: 10.1073/pnas.1417322111

The Li-Fraumeni syndrome (LFS) and its variant form (LFL) is a familial predisposition to multiple forms of childhood, adolescent, and adult cancers associated with germ-line mutation in the TP53 tumor suppressor gene. Individual disparities in tumor patterns are compounded by acceleration of cancer onset with successive generations. It has been suggested that this apparent anticipation pattern may result from germ-line genomic instability in TP53 mutation carriers, causing increased DNA copy-number variations (CNVs) with successive generations. To address the genetic basis of phenotypic disparities of LFS/LFL, we performed whole-genome sequencing (WGS) of 13 subjects from two generations of an LFS kindred. Neither de novo CNV nor significant difference in total CNV was detected in relation with successive generations or with age at cancer onset. These observations were consistent with an experimental mouse model system showing that trp53 deficiency in the germ line of father or mother did not increase CNV occurrence in the offspring. On the other hand, individual records on 1,771 TP53 mutation carriers from 294 pedigrees were compiled to assess genetic anticipation patterns (International Agency for Research on Cancer TP53 database). No strictly defined anticipation pattern was observed. Rather, in multigeneration families, cancer onset was delayed in older compared with recent generations. These observations support an alternative model for apparent anticipation in which rare variants from noncarrier parents may attenuate constitutive resistance to tumorigenesis in the offspring of TP53 mutation carriers with late cancer onset.

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