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Fulltext Whole-Genome Shotgun Sequencing of Mycobacterium abscessus M156, an Emerging Clinical Pathogen in Malaysia

Choo SW, Wong YL, Beh CY, Lokanathan N, Leong ML, Ong CS, et al.

Genome Announc, 2013 Jan;1(1).
PMID: 23405341 DOI: 10.1128/genomeA.00063-12

Mycobacterium abscessus is an emerging clinical pathogen commonly associated with non-tuberculous mycobacterial infections. We report herein the draft genome of M. abscessus strain M156.
Fulltext Universal Primers for Detection and Sequencing of Hepatitis B Virus Genomes across Genotypes A to G

Chook JB, Teo WL, Ngeow YF, Tee KK, Ng KP, Mohamed R

J Clin Microbiol, 2015 Jun;53(6):1831-5.
PMID: 25788548 DOI: 10.1128/JCM.03449-14

Hepatitis B virus (HBV) has been divided into 10 genotypes, A to J, based on an 8% nucleotide sequence divergence between genotypes. The conventional practice of using a single set of primers to amplify a near-complete HBV genome is hampered by its low analytical sensitivity. The current practice of using overlapping conserved primer sets to amplify a complete HBV genome in a clinical sample is limited by the lack of pan-primers to detect all HBV genotypes. In this study, we designed six highly conserved, overlapping primer sets to cover the complete HBV genome. We based our design on the sequences of 5,154 HBV genomes of genotypes A to I downloaded from the GenBank nucleotide database. These primer sets were tested on 126 plasma samples from Malaysia, containing genotypes A to D and with viral loads ranging from 20 to >79,780,000 IU/ml. The overall success rates for PCR amplification and sequencing were >96% and >94%, respectively. Similarly, there was 100% amplification and sequencing success when the primer sets were tested on an HBV reference panel of genotypes A to G. Thus, we have established primer sets that gave a high analytical sensitivity for PCR-based detection of HBV and a high rate of sequencing success for HBV genomes in most of the viral genotypes, if not all, without prior known sequence data for the particular genotype/genome.
Fulltext Tsukamurella tyrosinosolvens intravascular catheter-related bacteremia in a haematology patient: a case report

Karunakaran R, Halim HA, Ng KP, Hanifah YA, Chin E, Jaafar FL, et al.

Eur Rev Med Pharmacol Sci, 2011 Nov;15(11):1343-6.
PMID: 22195371

Tsukamurella spp. are a rare but important cause of intravascular catheter-related bacteremia in immunocompromised patients. The organism is an aerobic, Gram-positive, weakly acid-fast bacillus that is difficult to differentiate using standard laboratory methods from other aerobic actinomycetales such as Nocardia spp., Rhododoccus spp., Gordonia spp., and the rapid growing Mycobacterium spp. We report a case of Tsukamurella tyrosinosolvens catheter-related bacteremia in a 51-year-old haematology patient who responded to treatment with imipenem and subsequent line removal. 16srRNA sequencing allowed for the prompt identification of this organism.
Trends in obstetric anaesthesia and analgesia over a ten year period in the University Malaya Medical Centre, Kuala Lumpur

Chan YK, Ng KP, Chiu CL

Int J Obstet Anesth, 2002 Jul;11(3):176-9.
PMID: 15321544 DOI: 10.1054/ijoa.2002.0954

Available data for obstetric care in the University Malaya Medical Centre, Kuala Lumpur from 1987 to 1999 were reviewed. Despite incomplete data, we were able to determine fairly well the practice of obstetric anaesthesia and analgesia in the unit, and the changes over the years. There was a decline in the use of general anaesthesia for both elective and emergency caesarean sections from 41.3% and 69.4% respectively in 1995 to 21.6% and 26.9% respectively in 1999. By 1999, regional anaesthesia had become the most common method of anaesthesia administered in both elective (14.3% epidural and 63.5% spinal) and emergency (30.2% epidural and 42.6% spinal) caesarean sections. The percentage of patients delivering vaginally who received epidural analgesia appeared to have stabilised at about 8 to 9% in the last few years, with a gradual decline in the total instrumental delivery rate from a high of about 12% to the pre-epidural rate of 7%.
Fulltext The prevalence of cryptosporidiosis in children and adults at University Hospital, Kuala Lumpur

Ng KP, Shekhar KC

Med J Malaysia, 1993 Sep;48(3):293-6.
PMID: 8183141

A total of 320 faecal specimens obtained from 295 patients (192 children and 103 adults) with diarrhoea and 47 faecal specimens from healthy adults were screened for Cryptosporidium oocysts. Faecal specimens were first screened by modified Ziehl Neelsen stain and specimens with oocysts were confirmed by direct immunofluorescence technique. Cryptosporidium oocysts were detected in 4 children but not in normal healthy adults or in diarrhoeic adults.
Fulltext The prevalence of anti-HCV antibody in risk groups and blood donors

Ng KP, Saw TL, Wong NW, Goh KL, Chuah SY, Nagaratnam M

Med J Malaysia, 1995 Dec;50(4):302-5.
PMID: 8668047

Anti-HCV antibody was detected in 1.9% of the blood donors in University Hospital. Among the risk groups, 33.3% of the patients with post-transfusion hepatitis were tested positive for anti-HCV antibody. The anti-HCV antibody was detected in 30% of the IDU. Haemodialysis patients, patients with acute and chronic hepatitis and patients with liver cirrhosis appeared to have increased risk of Hepatitis C virus infection. The results indicate that the frequency of HCV infection increases with the exposure to blood or blood products.
The mycological and molecular study of Hortaea werneckii isolated from blood and splenic abscess

Ng KP, Soo-Hoo TS, Na SL, Tay ST, Hamimah H, Lim PC, et al.

Mycopathologia, 2005 Jun;159(4):495-500.
PMID: 15983734

Hortaea werneckii is an environmental dematiaceous fungus found in the halophilic environment. It causes tinea nigra. We report the isolation of H. werneckii from blood and splenic abscess of two patients with acute myelomonocytic leukaemia. H. werneckii grew at room temperature but not at 37 degrees C, it was identified by biochemical tests, growth characteristics and the presence of conspicuous collarette intercalary on dividing yeast cells. The use of specific oligonucleotide primer Hor-F (5'-TGGACACCTTCA TAACTCTTG-3') and Hor-R (5'-TCACAACGCTTAGAGACGG-3') confirmed the two isolates were H. werneckii. The sequence for 281 nucleotide of HW299 and HW403 were 99% identical but differed only in one nucleotide. In vitro anti-fungal susceptibility testing showed that the isolates were resistant to amphotericin B and flucytosine.
The manual MGIT system for the detection of M. tuberculosis in respiratory specimens: an experience in the University Malaya Medical Centre

Fadzilah MN, Ng KP, Ngeow YF

Malays J Pathol, 2009 Dec;31(2):93-7.
PMID: 20514851

A prospective study was conducted on 510 respiratory specimens for the presence of M. tuberculosis detected by direct acid-fast bacilli (AFB) smear examination, culture in the Manual Mycobacteria Growth Indicator Tube (BBL MGIT, Becton-Dickinson) and culture on Lowenstein-Jensen (LJ) medium. From positive BBL MGIT tubes, Ziehl-Neelsen and Gram stains were performed and subcultures were put up on LJ medium. A total of 101 (19.8%) specimens were positive by the BBL MGIT, 60 (11.8%) by primary LJ medium culture, 31 (6.1%) by direct smear examination and 29 (5.7%) by all three methods. Using primary LJ culture as the gold standard, the sensitivity and specificity of the BBL MGIT were 90% and 89.6% respectively but the sensitivity of AFB smear microscopy was only 48.3%. About half (51.1%) of the BBL MGIT false positives were due to contamination by non-AFB bacteria. The remaining false positives comprised specimens that were AFB microscopy positive but LJ culture negative. Of the AFB isolates obtained on LJ primary and sub-cultures, almost all (93.3%) were identified as Mycobacterium tuberculosis complex. The mean time-to-detection was significantly shorter (p < 0.0001) for the BBL MGIT than for LJ culture. For the former, positive results were available within 14 days for both AFB smear-positive and AFB smear-negative specimens. On the average, positive results were obtained 1.8 days earlier for direct AFB smear-positive samples than for AFB smear-negative samples. On the other hand, positive growth on LJ medium appeared after at least 33 days of incubation. These findings suggest that the BBL MGIT system will be a suitable alternative to LJ culture for the routine diagnosis of pulmonary tuberculosis, but a combination of liquid and solid cultures is still required for the highest diagnostic accuracy.
Fulltext The genome of newly classified Ochroconis mirabilis: Insights into fungal adaptation to different living conditions

Yew SM, Chan CL, Kuan CS, Toh YF, Ngeow YF, Na SL, et al.

BMC Genomics, 2016 Feb 03;17:91.
PMID: 26842951 DOI: 10.1186/s12864-016-2409-8

Ochroconis mirabilis, a recently introduced water-borne dematiaceous fungus, is occasionally isolated from human skin lesions and nails. We identified an isolate of O. mirabilis from a skin scraping with morphological and molecular studies. Its genome was then sequenced and analysed for genetic features related to classification and biological characteristics.
The evolving molecular epidemiology of HIV type 1 among injecting drug users (IDUs) in Malaysia

Tee KK, Saw TL, Pon CK, Kamarulzaman A, Ng KP

AIDS Res Hum Retroviruses, 2005 Dec;21(12):1046-50.
PMID: 16379608

Earlier studies in the 1990s indicate that human immunodeficiency virus type 1 (HIV-1) subtype B has been the predominant subtype among injecting drug users (IDUs) in Malaysia. More recent studies performed between 2003 and 2004, however, show a high prevalence of unique CRF01_AE/B intersubtype recombinants among IDUs. To determine the subtype distribution among IDUs in Kuala Lumpur prior to the emergence of CRF01_AE/B intersubtype recombinants, the gag-pol or the reverse transcriptase gene was sequenced from IDUs who were diagnosed as HIV positive between 1993 and 2002. Subtype B was present at 50.0% followed by CRF01_AE/B recombinant at 41.7%, with more CRF01_AE/B recombinants detected between 2000 and 2002. All CRF01_AE/B recombinants shared similar recombination patterns. Interestingly, we found that this potential new candidate of circulating recombinant form (CRF) could have emerged as early as the mid-1990s. The results showed evidence of changing HIV-1 molecular epidemiology toward the predominance of CRF01_AE/B intersubtype recombinants among IDUs in Kuala Lumpur.
Fulltext The diagnostic performance of a single GeneXpert MTB/RIF assay in an intensified tuberculosis case finding survey among HIV-infected prisoners in Malaysia

Al-Darraji HA, Abd Razak H, Ng KP, Altice FL, Kamarulzaman A

PLoS One, 2013;8(9):e73717.
PMID: 24040038 DOI: 10.1371/journal.pone.0073717

Delays in tuberculosis (TB) diagnosis, particularly in prisons, is associated with detrimental outcomes. The new GeneXpert MTB/RIF assay (Xpert) offers accurate and rapid diagnosis of active TB, but its performance in improving case detection in high-transmission congregate settings has yet to be evaluated. We assessed the diagnostic accuracy of a single Xpert assay in an intensified case finding survey among HIV-infected prisoners in Malaysia.
The Utility of Combined Urine Urea and Creatinine Clearance for Pretransplant Renal Function Assessment

Thye CK, Lee YW, Jalalonmuhali M, Lim SK, Ng KP

Transplant Proc, 2022 Feb 02.
PMID: 35123793 DOI: 10.1016/j.transproceed.2021.12.023

BACKGROUND: Evaluation of donor renal function as glomerular filtration rate (GFR) is a crucial part of pretransplant workup. Most guidelines recommend measured GFR (mGFR) using exogenous markers with creatinine clearance (CrCl) as an alternative. However, exogenous markers are difficult to obtain and perform, and CrCl may overestimate GFR.
OBJECTIVE: We explore the use of CrCl and combined urea and creatinine clearance as an alternative for GFR assessment.
METHODS: A retrospective study involving 81 kidney donors from 2007 to 2020, with mGFR collected by chromium 51-labeled ethylenediaminetetraacetic acid (51Cr-EDTA) and CrCl and combined urea and creatinine clearance. We analyzed the performance of CrCl and combined urea and creatinine clearance against 51Cr-EDTA. Adequacy of urine volume was taken into consideration.
RESULTS: A total of 81 candidates with a mean age of 44.80 ± 10.77 years were enrolled. Mean mGFR from 51Cr-EDTA was 123.66 ± 26.91 mL/min/1.73 m2, and combined urea and creatinine clearance and CrCl were 122.13 ± 47.07 and 133.40 ± 36.32 mL/min/1.73 m2, respectively. CrCl overestimated 51Cr-EDTA. Though combined urea and creatinine clearance had minimal bias, it had a lower correlation coefficient (0.25 vs 0.43), lower precision (49.51 vs 38.10), and slightly lower accuracy within 30% of 51Cr-EDTA (74.07% vs 76.54%).
CONCLUSIONS: Combined urea and creatinine clearance did not improve the performance of CrCl. Nevertheless, it can potentially be used as first-line GFR assessment, followed by mGFR in selected donors, to ascertain threshold of safe kidney donation. A stringent urine collection method is essential to ensure accurate measurement.
The Outcome of the Elderly Living Kidney Donors in a Single Tertiary Center in Malaysia

Goh ET, Jalalonmuhali M, Ng KP, Wan Md Adnan AH, Hing Wong A, Cheng SF, et al.

Transplant Proc, 2022 Feb 04.
PMID: 35131101 DOI: 10.1016/j.transproceed.2021.12.039

Living-kidney transplantation increases with years, however, the rate is comparatively low to support local needs. Marginal living donors like the elderly were used to increase the donor pool. We retrospectively evaluate the outcome of 25 elderly living kidney donors (eLKDs) who were ≥60 years old at the time of donation in our center. Their medical history and laboratory results were analyzed retrospectively from e-medical records. There are 16 females (64.0%) with a median age of 63 (60.5-66.0). The mean follow-up duration was 4.36 ± 2.46 years. Their mean body mass index increased from 23.70 ± 3.07 kg/m2 to 24.21 ± 2.93 kg/m2 (t[14] = -2.176, P = .047) post donation. Systolic blood pressure (SBP) increased from 133.33 ± 11.65 mm Hg to 140.56 ± 17.78 mm Hg (t[17] = -2.124, P = .049). However, the prevalence of overweight and hypertension were not significant. Only 5.56% of the eLKDs developed proteinuria post nephrectomy (P =1.000). Serum creatinine increased from 62.33 ± 14.39 mmol/L to 104.63 ± 28.53 mmol/L post 1-month donation (t[23] = -9.720, P = .000) and decreased to 99.67 ± 22.39 mmol/L post 1-year donation (t[17] = -8.415, P = .006), and latest results were 94.28 ± 20.74mmol/L (t[17] = -6.630, P = .033). Fasting blood glucose and HbA1c level recorded no significant changes post donation. We noted that 47.62% of the eLKDs had dyslipidemia pre donation, which increased to 76.20% post donation (P = .031). eLKDs with hyperuricemia increased significantly from 5.88% to 52.94%; with uric acid level from 306.12 ± 68.67 umol/L to 412.24 ± 74.14 umol/L (t[16] = -7.726, P = .000). None of the eLKDs were diagnosed with metabolic syndrome pre and post kidney donation. Postdonation kidney function of the eLKDs compensated well and were stable in the short term. We noted statistically significant increments of weight, body mass index, SBP, uric acid, and lipid levels, which did not translate to clinical significance post donation. Elderly living-kidney donation can be done safely with close monitoring post donation.
The Effects of Different Induction Regimes on Serial Lymphocyte Subsets in Kidney Transplant Recipients: A Single Tertiary Center Experience

Jalalonmuhali M, Ng KP, Lee YW, Gan CC, Hing Wong A, Wan Md Adnan WAH, et al.

Transplant Proc, 2022 Feb 15.
PMID: 35181166 DOI: 10.1016/j.transproceed.2022.01.004

BACKGROUND: Immunosuppressive therapy is the backbone of kidney transplantation in preventing acute rejection. T-cell depletion after doses of thymoglobulin is dose-dependent, as are their side effects. At the same time, basiliximab and other maintenance immunosuppressive drugs act at different signals on T lymphocytes. Therefore, studying the pattern of lymphocyte subset depletion depending on the induction regime given at transplantation could be an added tool in managing post-transplant recipients.
METHODOLOGY: This prospective observational study recruited kidney transplant recipients from August 2019 through April 2021 at the University of Malaya Medical Centre. Blood tests for lymphocyte subsets were taken at pre-transplant, 1 week, 1 month, 3 months, and 6 months post-transplantation. At transplantation, recipients received either basiliximab, low-dose thymoglobulin (cumulative dose: 1.5 mg/kg), or standard-dose thymoglobulin (cumulative dose: 5 mg/kg).
RESULTS: A total of 39 patients were recruited: 38.5% received basiliximab (15 of 39), 15.4% received low-dose thymoglobulin (6 of 39), and 46.2% received standard-dose thymoglobulin (18 of 39). Absolute lymphocyte counts 1 week post-transplantation were 1.5 ± 0.84 × 109/L for basiliximab, 0.7 ± 0.57 × 109/L for low-dose thymoglobulin, and 0.1 ± 0.08 × 109/L for standard-dose thymoglobulin (P < .001). The CD4+ and CD8+ counts were severely depleted in the standard-dose thymoglobulin group, with a statistically significant differenceup to 6 months post-transplantation. In the low-dose thymoglobulin group, the CD4+ and CD8+ counts were depleted at 1 week post-transplantation and recovered at 1 month post-transplantation. There was no difference in allograft function and incidence of allograft rejection across groups.
CONCLUSIONS: The effects on lymphocyte counts, CD4+ and CD8+, vary depending on the type and dose of induction immunosuppression. This could be a guiding tool in managing immunosuppression post-transplantation depending on the patient's immunologic risk.
Systemic Candida infection in University hospital 1997-1999: the distribution of Candida biotypes and antifungal susceptibility patterns

Ng KP, Saw TL, Na SL, Soo-Hoo TS

Mycopathologia, 2001;149(3):141-6.
PMID: 11307597

A total of 102 Candida species were isolated from blood cultures from January 1997 to October 1999. Using assimilation of carbohydrate test, 52 (51.0%) of the Candida sp. were identified as C. parapsilosis, 25.5% (26) were C. tropicalis. C. albicans made up 11.8% (12), 6.9% (7) were C. rugosa, 3.8% (4) C. glabrata and 1% (1) C. guilliermondii. No C. dubliniensis was found in the study. In vitro antifungal susceptibility tests showed that all Candida species were sensitive to nystatin, amphotericin B and ketoconazole. Although all isolates remained sensitive to fluconazole, intermediate susceptibility was found in 3 C. rugosa isolates. Antifungal agents with high frequency of resistance were econazole, clotrimazole, miconazole and 5-fluorocytosine. Candida species found to have resistance to these antifungal agents were non-C. albicans.
Strategies targeted at motivating unrelated living kidney donation

Tumin M, Noh A, Chong CS, Mohd Satar N, Lim SK, Abdullah N, et al.

Ann. Transplant., 2013;18:314-9.
PMID: 23792535 DOI: 10.12659/AOT.883957

This paper aimed to assess the willingness of Malaysians with post-secondary education to be living kidney donors.
Short communication: low prevalence of genotypic drug resistance mutations among antiretroviral-naive HIV type 1 patients in Malaysia

Tee KK, Kamarulzaman A, Ng KP

AIDS Res Hum Retroviruses, 2006 Feb;22(2):121-4.
PMID: 16478392

To assess the prevalence of mutations associated with drug resistance in antiretroviral-naive patients in Kuala Lumpur, Malaysia, genotypic resistance testing was conducted among drug-naive HIV-1 patients attending the University Malaya Medical Center (UMMC) between July 2003 and June 2004. Reverse transcriptase (RT) and protease genes of plasma virions were sequenced from 100 individuals. The majority of the patients were recently diagnosed. Codons 20-255 of the RT and 1-96 of the protease gene were examined for major and minor mutations associated with antiretroviral resistance reported by the International AIDS Society- USA (IAS-USA) Drug Resistance Mutations Group. The prevalence of patients with at least one major mutation conferring drug resistance was 1%, with only one patient having a Y181C amino acid substitution in the RT gene that confers high-level resistance to nevirapine and delavirdine. Minor mutations were detected in high prevalence in the protease gene. Amino acid substitutions I13V, E35D, and M36I were associated with CRF01_AE while L63P, V77I, and I93L were associated with subtype B. Baseline prevalence of major mutations associated with resistance to antiretroviral drugs was low among antiretroviral-naive HIV-1 patients, suggesting that routine drug resistance testing may be unnecessary for all individuals newly diagnosed with HIV or all patients beginning antiretroviral therapy.
Fulltext Seroprevalence of anti-HCV in an urban child population: a preliminary study from Kuala Lumpur

Lee WS, Ng KP

Singapore Med J, 2001 Mar;42(3):100-1.
PMID: 11405558

A pilot study to determine the seroprevalence of anti-HCV among children from Kuala Lumpur, Malaysia, was conducted using microparticle enzyme immunoassay. Serum samples were obtained randomly from children, aged between one to 16 years of age, admitted to the paediatric unit of University of Malaya Medical Centre, Kuala Lumpur for various medical reasons. Of the 179 samples assayed, only one was positive, giving the prevalence rate of 0.6%. It is reasonable to conclude that the seroprevalence of anti-HCV among children from Kuala Lumpur is low, less than 1%.
Fulltext Sequencing of Cladosporium sphaerospermum, a Dematiaceous fungus isolated from blood culture

Ng KP, Yew SM, Chan CL, Soo-Hoo TS, Na SL, Hassan H, et al.

Eukaryotic Cell, 2012 May;11(5):705-6.
PMID: 22544899 DOI: 10.1128/EC.00081-12

Cladosporium sphaerospermum is one of the most widely distributed allergens causing serious problems in patients with respiratory tract disease. We report the 26,644,473-bp draft genome sequence and gene annotation of C. sphaerospermum UM843. Analysis of the genome sequence led to the finding of genes associated with C. sphaerospermum's melanin biosynthesis, allergens, and antifungal drug resistance.
Fulltext Scopulariopsis brevicaulis infection in a patient with acute myeloid leukemia

Ng KP, Soo-Hoo TS, Na SL, Gan GG, Sangkar JV, Teh AKH

Med J Malaysia, 2003 Oct;58(4):608-12.
PMID: 15190640

Scopulariopsis brevicaulis is a soil fungus normally associated with onychomycosis. It causes subcutaneous infection in immunocompromised patients and is rarely isolated from blood. A case of systemic Scopulariopsis brevicaulis infection was reported in a patient with acute myeloid leukemia. The patient developed persistent fever that did not respond to wide spectrum antibiotics and amphotericin B. Scopulariopsis brevicaulis was the only pathogen isolated from blood cultures. The fever subsided with itraconazole and there was no recurrence of fungal infection with prolonged maintenance of oral itraconazole.

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