MyMedR

Fulltext Nucleic Acid-Based Diagnostic Tests for the Detection SARS-CoV-2: An Update

Yu CY, Chan KG, Yean CY, Ang GY

Diagnostics (Basel), 2021 Jan 01;11(1).

PMID: 33401392 DOI: 10.3390/diagnostics11010053

The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began as a cluster of pneumonia cases in Wuhan, China before spreading to over 200 countries and territories on six continents in less than six months. Despite rigorous global containment and quarantine efforts to limit the transmission of the virus, COVID-19 cases and deaths have continued to increase, leaving devastating impacts on the lives of many with far-reaching effects on the global society, economy and healthcare system. With over 43 million cases and 1.1 million deaths recorded worldwide, accurate and rapid diagnosis continues to be a cornerstone of pandemic control. In this review, we aim to present an objective overview of the latest nucleic acid-based diagnostic tests for the detection of SARS-CoV-2 that have been authorized by the Food and Drug Administration (FDA) under emergency use authorization (EUA) as of 31 October 2020. We systematically summarize and compare the principles, technologies, protocols and performance characteristics of amplification- and sequencing-based tests that have become alternatives to the CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel. We highlight the notable features of the tests including authorized settings, along with the advantages and disadvantages of the tests. We conclude with a brief discussion on the current challenges and future perspectives of COVID-19 diagnostics.

Fulltext Immobilization of α-Amylase from Anoxybacillus sp. SK3-4 on ReliZyme and Immobead Supports

Kahar UM, Sani MH, Chan KG, Goh KM

Molecules, 2016 Sep 09;21(9).

PMID: 27618002 DOI: 10.3390/molecules21091196

α-Amylase from Anoxybacillus sp. SK3-4 (ASKA) is a thermostable enzyme that produces a high level of maltose from starches. A truncated ASKA (TASKA) variant with improved expression and purification efficiency was characterized in an earlier study. In this work, TASKA was purified and immobilized through covalent attachment on three epoxide (ReliZyme EP403/M, Immobead IB-150P, and Immobead IB-150A) and an amino-epoxide (ReliZyme HFA403/M) activated supports. Several parameters affecting immobilization were analyzed, including the pH, temperature, and quantity (mg) of enzyme added per gram of support. The influence of the carrier surface properties, pore sizes, and lengths of spacer arms (functional groups) on biocatalyst performances were studied. Free and immobilized TASKAs were stable at pH 6.0-9.0 and active at pH 8.0. The enzyme showed optimal activity and considerable stability at 60 °C. Immobilized TASKA retained 50% of its initial activity after 5-12 cycles of reuse. Upon degradation of starches and amylose, only immobilized TASKA on ReliZyme HFA403/M has comparable hydrolytic ability with the free enzyme. To the best of our knowledge, this is the first report of an immobilization study of an α-amylase from Anoxybacillus spp. and the first report of α-amylase immobilization using ReliZyme and Immobeads as supports.

Fulltext Whole-genome Sequencing of Vibrio sinaloensis T47, a Tropical Marine Isolate with Quorum Sensing Properties

Mohamad NI, How KY, Yin WF, Chan KG

J Genomics, 2017;5:48-50.

PMID: 28348643 DOI: 10.7150/jgen.16163

A large number of Vibrio sp. thrive in the marine environment and they are notable to cause food borne infection associated with undercooked seafood. In this study, we report the whole genome sequence of Vibrio sinaloensis T47 which was isolated from coastal marine water in Morib Beach, Hulu Selangor. The genome is made up of approximately 4.59 Mbp with 80 contigs and 46% G+C content. From the annotated genome, genes associated with quorum sensing (QS) were identified. This research provides a genetic basis for better understanding of QS pathway which contributes to the physiological traits of strain T47 to thrive in the marine environment.

Characterization and Comparative Overview of Complete Sequences of the First Plasmids of Pandoraea across Clinical and Non-clinical Strains

Yong D, Tee KK, Yin WF, Chan KG

Front Microbiol, 2016;7:1606.

PMID: 27790203

To date, information on plasmid analysis in Pandoraea spp. is scarce. To address the gap of knowledge on this, the complete sequences of eight plasmids from Pandoraea spp. namely Pandoraea faecigallinarum DSM 23572(T) (pPF72-1, pPF72-2), Pandoraea oxalativorans DSM 23570(T) (pPO70-1, pPO70-2, pPO70-3, pPO70-4), Pandoraea vervacti NS15 (pPV15) and Pandoraea apista DSM 16535(T) (pPA35) were studied for the first time in this study. The information on plasmid sequences in Pandoraea spp. is useful as the sequences did not match any known plasmid sequence deposited in public databases. Replication genes were not identified in some plasmids, a situation that has led to the possibility of host interaction involvement. Some plasmids were also void of par genes and intriguingly, repA gene was also not discovered in these plasmids. This further leads to the hypothesis of host-plasmid interaction. Plasmid stabilization/stability protein-encoding genes were observed in some plasmids but were not established for participating in plasmid segregation. Toxin-antitoxin systems MazEF, VapBC, RelBE, YgiT-MqsR, HigBA, and ParDE were identified across the plasmids and their presence would improve plasmid maintenance. Conjugation genes were identified portraying the conjugation ability amongst Pandoraea plasmids. Additionally, we found a shared region amongst some of the plasmids that consists of conjugation genes. The identification of genes involved in replication, segregation, toxin-antitoxin systems and conjugation, would aid the design of drugs to prevent the survival or transmission of plasmids carrying pathogenic properties. Additionally, genes conferring virulence and antibiotic resistance were identified amongst the plasmids. The observed features in the plasmids shed light on the Pandoraea spp. as opportunistic pathogens.

Fulltext Exploring the Role and Potential of Probiotics in the Field of Mental Health: Major Depressive Disorder

Johnson D, Thurairajasingam S, Letchumanan V, Chan KG, Lee LH

Nutrients, 2021 May 20;13(5).

PMID: 34065187 DOI: 10.3390/nu13051728

The field of probiotic has been exponentially expanding over the recent decades with a more therapeutic-centered research. Probiotics mediated microbiota modulation within the microbiota-gut-brain axis (MGBA) have been proven to be beneficial in various health domains through pre-clinical and clinical studies. In the context of mental health, although probiotic research is still in its infancy stage, the promising role and potential of probiotics in various mental disorders demonstrated via in-vivo and in-vitro studies have laid a strong foundation for translating preclinical models to humans. The exploration of the therapeutic role and potential of probiotics in major depressive disorder (MDD) is an extremely noteworthy field of research. The possible etio-pathological mechanisms of depression involving inflammation, neurotransmitters, the hypothalamic-pituitary-adrenal (HPA) axis and epigenetic mechanisms potentially benefit from probiotic intervention. Probiotics, both as an adjunct to antidepressants or a stand-alone intervention, have a beneficial role and potential in mitigating anti-depressive effects, and confers some advantages compared to conventional treatments of depression using anti-depressants.

Fulltext Quorum sensing activity of Aeromonas caviae strain YL12, a bacterium isolated from compost

Lim YL, Ee R, Yin WF, Chan KG

Sensors (Basel), 2014 Apr 22;14(4):7026-40.

PMID: 24759107 DOI: 10.3390/s140407026

Quorum sensing is a well-studied cell-to-cell communication method that involves a cell-density dependent regulation of genes expression mediated by signalling molecules. In this study, a bacterium isolated from a plant material compost pile was found to possess quorum sensing activity based on bioassay screening. Isolate YL12 was identified using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and molecular typing using rpoD gene which identified the isolate as Aeromonas caviae. High resolution tandem mass spectrometry was subsequently employed to identify the N-acyl homoserine lactone profile of Aeromonas caviae YL12 and confirmed that this isolate produced two short chain N-acyl homoserine lactones, namely C4-HSL and C6, and the production was observed to be cell density-dependent. Using the thin layer chromatography (TLC) bioassay, both AHLs were found to activate C. violaceum CV026, whereas only C6-HSL was revealed to induce bioluminescence expression of E. coli [pSB401]. The data presented in this study will be the leading steps in understanding the role of quorum sensing in Aeromonas caviae strain YL12.

Fulltext Draft Genome Sequence of Quorum-Sensing and Quorum-Quenching Pseudomonas aeruginosa Strain MW3a

Chan KG, Wong CS, Yin WF, Chan XY

Genome Announc, 2014;2(2).

PMID: 24744329 DOI: 10.1128/genomeA.00258-14

Pseudomonas aeruginosa has a broad range of habitation, from aquatic environments to human lungs. The coexistence of quorum-sensing and quorum-quenching activities occurs in P. aeruginosa strain MW3a. In this work, we present the draft genome sequence of P. aeruginosa MW3a, an interesting bacterium isolated from a marine environment.

Fulltext De Novo Assembly of the Quorum-Sensing Pandoraea sp. Strain RB-44 Complete Genome Sequence Using PacBio Single-Molecule Real-Time Sequencing Technology

Ee R, Lim YL, Yin WF, Chan KG

Genome Announc, 2014;2(2).

PMID: 24699956 DOI: 10.1128/genomeA.00245-14

We report the first complete genome sequence of Pandoraea sp. strain RB-44, which was found to possess quorum-sensing properties. To the best of our knowledge, this is the first documentation of both a complete genome sequence and quorum-sensing properties of a Pandoraea species.

Fulltext Caffeine as a potential quorum sensing inhibitor

Norizan SN, Yin WF, Chan KG

Sensors (Basel), 2013;13(4):5117-29.

PMID: 23598500 DOI: 10.3390/s130405117

Quorum sensing enables bacteria to control the gene expression in response to the cell density. It regulates a variety of bacterial physiological functions such as biofilm formation, bioluminescence, virulence factors and swarming which has been shown contribute to bacterial pathogenesis. The use of quorum sensing inhibitor would be of particular interest in treating bacterial pathogenicity and infections. In this work, we have tested caffeine as quorum sensing inhibitor by using Chromobacterium violaceum CV026 as a biosensor. We verified that caffeine did not degrade the N-acyl homoserine lactones tested. In this work, it is shown that caffeine could inhibit N-acyl homoserine lactone production and swarming of a human opportunistic pathogen, namely Pseudomonas aeruginosa PA01. To the best of our knowledge, this is the first documentation providing evidence on the presence of anti-quorum sensing activity in caffeine. Our work will allow caffeine to be explored as anti-infective drugs.

Fulltext Long chain N-acyl homoserine lactone production by Enterobacter sp. isolated from human tongue surfaces

Yin WF, Purmal K, Chin S, Chan XY, Chan KG

Sensors (Basel), 2012;12(11):14307-14.

PMID: 23202161 DOI: 10.3390/s121114307

We report the isolation of N-acyl homoserine lactone-producing Enterobacter sp. isolate T1-1 from the posterior dorsal surfaces of the tongue of a healthy individual. Spent supernatants extract from Enterobacter sp. isolate T1-1 activated the biosensor Agrobacterium tumefaciens NTL4(pZLR4), suggesting production of long chain AHLs by these isolates. High resolution mass spectrometry analysis of these extracts confirmed that Enterobacter sp. isolate T1-1 produced a long chain N-acyl homoserine lactone, namely N-dodecanoyl-homoserine lactone (C12-HSL). To the best of our knowledge, this is the first isolation of Enterobacter sp., strain T1-1 from the posterior dorsal surface of the human tongue and N-acyl homoserine lactones production by this bacterium.

Fulltext Insights from the genome sequence of quorum-quenching Staphylococcus sp. strain AL1, isolated from traditional Chinese soy sauce brine fermentation

Chong TM, Tung HJ, Yin WF, Chan KG

J Bacteriol, 2012 Dec;194(23):6611-2.

PMID: 23144375 DOI: 10.1128/JB.01669-12

We report the draft genome sequence of Staphylococcus sp. strain AL1, which degrades quorum-sensing molecules (namely, N-acyl homoserine lactones). To the best of our knowledge, this is the first documentation that reports the whole genome sequence and quorum-quenching activity of Staphylococcus sp. strain AL1.

Fulltext Genome sequence of Roseomonas sp. strain B5, a quorum-quenching N-acylhomoserine lactone-degrading bacterium isolated from Malaysian tropical soil

Chen JW, Gan HM, Yin WF, Chan KG

J Bacteriol, 2012 Dec;194(23):6681-2.

PMID: 23144419 DOI: 10.1128/JB.01866-12

Roseomonas sp. strain B5 was isolated from Malaysian tropical soil that showed N-acylhomoserine lactone degradation. This is the first genome announcement of a member from the genus of Roseomonas and the first report on the quorum-quenching activity of Roseomonas spp.

A novel medium for the isolation of N-acylhomoserine lactone-degrading bacteria

Chan KG, Yin WF, Sam CK, Koh CL

J Ind Microbiol Biotechnol, 2009 Feb;36(2):247-51.

PMID: 18946694 DOI: 10.1007/s10295-008-0491-x

A novel chemically defined medium, named KG medium, supplemented with N-3-oxo-hexanoylhomoserine lactone (3-oxo-C6-HSL), an acylhomoserine lactone (AHL) used as signalling molecules in Gram-negative bacterial cell-to-cell communication, as the sole source of carbon and nitrogen, was designed and successfully used for the enrichment and isolation of AHL-degrading bacteria. A 3-oxo-C6-HSL-degrading bacterium, 13sw7, was isolated from sewage after six enrichment transfers in the 3-oxo-C6-HSL-containing KG medium. On the basis of the almost complete 16S ribosomal DNA sequence, isolate 13sw7 was clustered with unculturable beta-proteobacteria. This study indicates that the AHL-containing KG medium is effective in isolating AHL-degrading bacteria, including those previously considered unculturable, from environmental sources. To the best of our knowledge, this is the first documentation of the isolation of an AHL-degrading proteobacterium from sewage.

Fulltext Microbial contamination of orthodontic buccal tubes from manufacturers

Purmal K, Chin S, Pinto J, Yin WF, Chan KG

Int J Mol Sci, 2010 Sep 16;11(9):3349-56.

PMID: 20957099 DOI: 10.3390/ijms11093349

This study aimed to test the sterility of new unused orthodontic buccal tubes received from manufacturers. Four different types of buccal tubes were used straight from the manufactures package without any additional sterilizing step. Of these buccal tubes tested, three genera of bacteria, implicated as opportunistic pathogens, namely Micrococcus luteus, Staphylococcus haemolyticus and Acinetobacter calcoaceticus were recovered from these buccal tubes. Our data showing microbial contamination on buccal tubes highlights the need of sterilization before clinical use. We also suggest that manufacturers should list the sterility state of orthodontic buccal tubes on their packaging or instructions stating the need for sterilization.

Treatment costs for patients with Streptococcus suis infection in Northern Thailand: a hospital-based observational study of 14-year data

Rayanakorn A, Katip W, Ademi Z, Chan KG

BMC Public Health, 2023 Apr 21;23(1):737.

PMID: 37085811 DOI: 10.1186/s12889-023-15623-w

BACKGROUND: Streptococcus suis (S.suis) is a neglected zoonotic disease that imposes a significant economic burden on healthcare and society. To our knowledge, studies estimating the cost of illness associated with S.suis treatment are limited, and no study focuses on treatment costs and potential key drivers in Thailand. This study aimed to estimate the direct medical costs associated with S.suis treatment in Thailand and identify key drivers affecting high treatment costs from the provider's perspective.

METHODS: A retrospective analysis of the 14-year data from 2005-2018 of confirmed S.suis patients admitted at Chiang Mai University Hospital (CMUH) was conducted. Descriptive statistics were used to summarize the data of patients' characteristics, healthcare utilization and costs. The multiple imputation with predictive mean matching strategy was employed to deal with missing Glasgow Coma Scale (GCS) data. Generalized linear models (GLMs) were used to forecast costs model and identify determinants of costs associated with S.suis treatment. The modified Park test was adopted to determine the appropriate family. All costs were inflated applying the consumer price index for medical care and presented to the year 2019.

RESULTS: Among 130 S.suis patients, the average total direct medical cost was 12,4675 Thai baht (THB) (US$ 4,016), of which the majority of expenses were from the "others" category (room charges, staff services and medical devices). Infective endocarditis (IE), GCS, length of stay, and bicarbonate level were significant predictors associated with high total treatment costs. Overall, marginal increases in IE and length of stay were significantly associated with increases in the total costs (standard error) by 132,443 THB (39,638 THB) and 5,490 THB (1,715 THB), respectively. In contrast, increases in GCS and bicarbonate levels were associated with decreases in the total costs (standard error) by 13,118 THB (5,026 THB) and 7,497 THB (3,430 THB), respectively.

CONCLUSIONS: IE, GCS, length of stay, and bicarbonate level were significant cost drivers associated with direct medical costs. Patients' clinical status during admission significantly impacts the outcomes and total treatment costs. Early diagnosis and timely treatment were paramount to alleviate long-term complications and high healthcare expenditures.

Fulltext Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine

Sulaiman J, Gan HM, Yin WF, Chan KG

Front Microbiol, 2014;5:556.

PMID: 25400624 DOI: 10.3389/fmicb.2014.00556

The quality of traditional Chinese soy sauce is determined by microbial communities and their inter-related metabolic roles in the fermentation tank. In this study, traditional Chinese soy sauce brine samples were obtained periodically to monitor the transitions of the microbial population and functional properties during the 6 months of fermentation process. Whole genome shotgun method revealed that the fermentation brine was dominated by the bacterial genus Weissella and later dominated by the fungal genus Candida. Metabolic reconstruction of the metagenome sequences demonstrated a characteristic profile of heterotrophic fermentation of proteins and carbohydrates. This was supported by the detection of ethanol with stable decrease of pH values. To the best of our knowledge, this is the first study that explores the temporal changes in microbial successions over a period of 6 months, through metagenome shotgun sequencing in traditional Chinese soy sauce fermentation and the biological processes therein.

Fulltext Complete Genome Sequence of Dyella japonica Strain A8 Isolated from Malaysian Tropical Soil

Hui RK, Chen JW, Chan KG, Leung FC

Genome Announc, 2014;2(6).

PMID: 25395638 DOI: 10.1128/genomeA.01164-14

We previously identified and presented the draft genome of a Xanthomonadaceae bacterial strain Dyella japonica A8 which shows quorum-quenching activity. Here, we report the complete, closed genome sequence of this bacterium. This complete genome may help to further investigate the comparative quorum-quenching activity among D. japonica strains.

Fulltext Antibacterial Mode of Action of Cinnamomum verum Bark Essential Oil, Alone and in Combination with Piperacillin, Against a Multi-Drug-Resistant Escherichia coli Strain

Yap PS, Krishnan T, Chan KG, Lim SH

J Microbiol Biotechnol, 2015 Aug;25(8):1299-306.

PMID: 25381741 DOI: 10.4014/jmb.1407.07054

This study aimed to investigate the mechanism of action of the cinnamon bark essential oil (CB), when used singly and also in combination with piperacillin, for its antimicrobial and synergistic activity against beta-lactamase TEM-1 plasmid-conferred Escherichia coli J53 R1. Viable count of this combination showed a complete killing profile at 20 h and further confirmed its synergistic effect by reducing the bacteria cell numbers. Analysis on the stability of treated cultures for cell membrane permeability by CB when tested against sodium dodecyl sulfate revealed that the bacterial cell membrane was disrupted by the essential oils. Scanning electron microscopy observation and bacterial surface charge measurement also revealed that CB causes irreversible membrane damage and reduces the bacterial surface charge. In addition, bioluminescence expression of Escherichia coli [pSB1075] and E. coli [pSB401] by CB showed reduction, indicating the possibility of the presence of quorum sensing (QS) inhibitors. Gas-chromatography and mass spectrometry of the essential oil of Cinnamomum verum showed that trans-cinnamaldehyde (72.81%), benzyl alcohol (12.5%), and eugenol (6.57%) were the major components in the essential oil. From this study, CB has the potential to reverse E. coli J53 R1 resistance to piperacillin through two pathways; modification in the permeability of the outer membrane or bacterial QS inhibition.

Fulltext Complete Genome Sequence of Cedecea neteri Strain SSMD04, a Bacterium Isolated from Pickled Mackerel Sashimi

Chan KG, Tan KH, Yin WF, Tan JY

Genome Announc, 2014;2(6).

PMID: 25523782 DOI: 10.1128/genomeA.01339-14

We report here the complete genome sequence of C. neteri SSMD04, a strain isolated from pickled mackerel sashimi, sequenced by third-generation sequencing technology. To the best of our knowledge, this is the first documentation that reports the complete genome of Cedecea neteri.

Fulltext Complete Genome Sequence of Pluralibacter gergoviae FB2, an N-Acyl Homoserine Lactone-Degrading Strain Isolated from Packed Fish Paste

Chan KG, Tee KK, Yin WF, Tan JY

Genome Announc, 2014;2(6).

PMID: 25502672 DOI: 10.1128/genomeA.01276-14

Pluralibacter gergoviae FB2, a bacterial strain isolated from packed food, has been found to exhibit quorum-quenching properties. Hence, we report the first, complete genome of P. gergoviae sequenced using the Pacific Biosciences single-molecule, real-time (SMRT) platform.

Displaying publications 41 - 60 of 372 in total