MyMedR

Fulltext Gene clusters of Hafnia alvei strain FB1 important in survival and pathogenesis: a draft genome perspective

Tan JY, Yin WF, Chan KG

Gut Pathog, 2014;6:29.

PMID: 25075225 DOI: 10.1186/1757-4749-6-29

Hafnia alvei is an opportunistic pathogen involved in various types of nosocomical infections. The species has been found to inhabit food and mammalian guts. However, its status as an enteropathogen, and whether the food-inhabiting strains could be a source of gastrointestinal infection remains obscure. In this report we present a draft genome of H. alvei strain FB1 isolated from fish paste meatball, a food popular among Malaysian and Chinese populations. The data was generated on the Illumina MiSeq platform.

Fulltext Genetic Characterization of a Novel HIV-1 Circulating Recombinant Form (CRF74_01B) Identified among Intravenous Drug Users in Malaysia: Recombination History and Phylogenetic Linkage with Previously Defined Recombinant Lineages

Cheong HT, Chow WZ, Takebe Y, Chook JB, Chan KG, Al-Darraji HA, et al.

PLoS One, 2015;10(7):e0133883.

PMID: 26196131 DOI: 10.1371/journal.pone.0133883

In many parts of Southeast Asia, the HIV-1 epidemic has been driven by the sharing of needles and equipment among intravenous drug users (IDUs). Over the last few decades, many studies have proven time and again that the diversity of HIV-1 epidemics can often be linked to the route of infection transmission. That said, the diversity and complexity of HIV-1 molecular epidemics in the region have been increasing at an alarming rate, due in part to the high tendency of the viral RNA to recombine. This scenario was exemplified by the discovery of numerous circulating recombinant forms (CRFs), especially in Thailand and Malaysia. In this study, we characterized a novel CRF designated CRF74_01B, which was identified in six epidemiologically unlinked IDUs in Kuala Lumpur, Malaysia. The near-full length genomes were composed of CRF01_AE and subtype B', with eight breakpoints dispersed in the gag-pol and nef regions. Remarkably, this CRF shared four and two recombination hotspots with the previously described CRF33_01B and the less prevalent CRF53_01B, respectively. Genealogy-based Bayesian phylogenetic analysis of CRF74_01B genomic regions showed that it is closely related to both CRF33_01B and CRF53_01B. This observation suggests that CRF74_01B was probably a direct descendent from specific lineages of CRF33_01B, CRF53_01B and subtype B' that could have emerged in the mid-1990s. Additionally, it illustrated the active recombination processes between prevalent HIV-1 subtypes and recombinants in Malaysia. In summary, we report a novel HIV-1 genotype designated CRF74_01B among IDUs in Kuala Lumpur, Malaysia. The characterization of the novel CRF74_01B is of considerable significance towards the understanding of the genetic diversity and population dynamics of HIV-1 circulating in the region.

Fulltext Genetic diversity of Coxsackievirus A21 associated with sporadic cases of acute respiratory infections in Malaysia

Supian NI, Ng KT, Chook JB, Takebe Y, Chan KG, Tee KK

BMC Infect Dis, 2021 May 17;21(1):446.

PMID: 34001016 DOI: 10.1186/s12879-021-06148-x

BACKGROUND: Coxsackievirus A21 (CVA21), a member of Enterovirus C from the Picornaviridae family, has been associated with respiratory illnesses in humans.

METHODS: A molecular epidemiological investigation of CVA21 was conducted among patients presenting with acute upper respiratory illnesses in the ambulatory settings between 2012 and 2014 in Kuala Lumpur, Malaysia.

RESULTS: Epidemiological surveillance of acute respiratory infections (n = 3935) showed low-level detection of CVA21 (0.08%, 1.4 cases/year) in Kuala Lumpur, with no clear seasonal distribution. Phylogenetic analysis of the new complete genomes showed close relationship with CVA21 strains from China and the United States. Spatio-temporal mapping of the VP1 gene determined 2 major clusters circulating worldwide, with inter-country lineage migration and strain replacement occurring over time.

CONCLUSIONS: The study highlights the emerging role of CVA21 in causing sporadic acute respiratory outbreaks.

Fulltext Genetic diversity, seasonality and transmission network of human metapneumovirus: identification of a unique sub-lineage of the fusion and attachment genes

Chow WZ, Chan YF, Oong XY, Ng LJ, Nor'E SS, Ng KT, et al.

Sci Rep, 2016 06 09;6:27730.

PMID: 27279080 DOI: 10.1038/srep27730

Human metapneumovirus (HMPV) is an important viral respiratory pathogen worldwide. Current knowledge regarding the genetic diversity, seasonality and transmission dynamics of HMPV among adults and children living in tropical climate remains limited. HMPV prevailed at 2.2% (n = 86/3,935) among individuals presented with acute respiratory tract infections in Kuala Lumpur, Malaysia between 2012 and 2014. Seasonal peaks were observed during the northeast monsoon season (November-April) and correlated with higher relative humidity and number of rainy days (P

Fulltext Genome Anatomy of Streptococcus parasanguinis Strain C1A, Isolated from a Patient with Acute Exacerbation of Chronic Obstructive Pulmonary Disease, Reveals Unusual Genomic Features

Chan KG, Ng KT, Pang YK, Chong TM, Kamarulzaman A, Yin WF, et al.

Genome Announc, 2015;3(3).

PMID: 26021924 DOI: 10.1128/genomeA.00541-15

Streptococcus parasanguinis causes invasive diseases. However, the mechanism by which it causes disease remains unclear. Here, we describe the complete genome sequence of S. parasanguinis C1A, isolated from a patient diagnosed with an acute exacerbation of chronic obstructive pulmonary disease. Several genes that might be associated with pathogenesis are also described.

Fulltext Genome Sequence Analysis Reveals Evidence of Quorum-Sensing Genes Present in Aeromonas hydrophila Strain M062, Isolated from Freshwater

Chan KG, Tan WS, Chang CY, Yin WF, Mumahad Yunos NY

Genome Announc, 2015;3(2).

PMID: 25767237 DOI: 10.1128/genomeA.00100-15

Aeromonas hydrophila has emerged worldwide as a human pathogen. Here, we report the draft whole-genome sequence of a freshwater isolate from Malaysia, A. hydrophila strain M062, and its N-acylhomoserine lactone genes are also reported here.

Fulltext Genome Sequence of Anoxybacillus thermarum AF/04T, Isolated from the Euganean Hot Springs in Abano Terme, Italy

Poli A, Nicolaus B, Chan KG, Kahar UM, Chan CS, Goh KM

Genome Announc, 2015;3(3).

PMID: 25999577 DOI: 10.1128/genomeA.00490-15

Anoxybacillus thermarum AF/04(T) was isolated from the Euganean hot springs in Abano Terme, Italy. The present work reports a high-quality draft genome sequence of strain AF/04(T). This work also provides useful insights into glycoside hydrolases, glycoside transferases, and sugar transporters that may be involved in cellular carbohydrate metabolism.

Fulltext Genome Sequence of Complex HIV-1 Unique Recombinant Forms Sharing a Common Recombination Breakpoint Identified in Malaysia

Cheong HT, Ng KT, Ong LY, Takebe Y, Chan KG, Koh C, et al.

Genome Announc, 2015;3(6).

PMID: 26543107 DOI: 10.1128/genomeA.01220-15

Three strains of HIV-1 unique recombinant forms (URFs) descended from subtypes B, B', and CRF01_AE were identified among people who inject drugs in Kuala Lumpur, Malaysia. These three URFs shared a common recombination breakpoint in the reverse transcriptase region, indicating frequent linkage within the drug-injecting networks in Malaysia.

Genome Sequence of Vibrio parahaemolyticus VP103 Strain Isolated from Shrimp in Malaysia

Letchumanan V, Ser HL, Chan KG, Goh BH, Lee LH

Front Microbiol, 2016;7:1496.

PMID: 27708636

Fulltext Genome Sequence of Vibrio parahaemolyticus VP152 Strain Isolated from Penaeus indicus in Malaysia

Letchumanan V, Ser HL, Tan WS, Ab Mutalib NS, Goh BH, Chan KG, et al.

Front Microbiol, 2016;7:1410.

PMID: 27656174 DOI: 10.3389/fmicb.2016.01410

Fulltext Genome Sequence of a Complex HIV-1 Unique Recombinant Form Involving CRF01_AE, Subtype B, and Subtype B' Identified in Malaysia

Chow WZ, Nizam S, Ong LY, Ng KT, Chan KG, Takebe Y, et al.

Genome Announc, 2014;2(2).

PMID: 24675847 DOI: 10.1128/genomeA.00139-14

A complex HIV-1 unique recombinant form involving subtypes CRF01_AE, B, and B' was recently identified from an injecting drug user in Malaysia. A total of 13 recombination breakpoints were mapped across the near-full-length genome of isolate 10MYPR226, indicating the increasingly diverse molecular epidemiology and frequent linkage among various high-risk groups.

Fulltext Genome Sequence of a Novel HIV-1 Circulating Recombinant Form (CRF77_cpx) Identified among Blood Donors in Malaysia

Tee KK, Bon AH, Chow WZ, Ng KT, Chan KG, Kamarulzaman A, et al.

Genome Announc, 2017 Jun 29;5(26).

PMID: 28663289 DOI: 10.1128/genomeA.00459-17

We report here the first HIV-1 circulating recombinant form (CRF) complex identified among the blood donors in Malaysia. The CRF77_cpx mosaic genome consists of parental subtypes B', C, and CRF01_AE and is structurally related to CRF07_BC. The identification of CRF77_cpx underlines the genetic complexity and mobility of HIV-1 among the blood donors.

Fulltext Genome Sequences of Two Pandoraea pnomenusa Isolates Recovered 11 Months Apart from a Cystic Fibrosis Patient

Ee R, Ambrose M, Lazenby J, Williams P, Chan KG, Roddam L

Genome Announc, 2015;3(1).

PMID: 25657265 DOI: 10.1128/genomeA.01389-14

Pandoraea is an emerging respiratory pathogen capable of causing chronic lung infections in people with cystic fibrosis (CF), but the clinical significance of this infection is ambiguous. We have sequenced and annotated the genomes of two multidrug-resistant Pandoraea pnomenusa isolates recovered 11 months apart from the same CF patient.

Fulltext Genome analysis of quorum sensing Cedecea neteri SSMD04 leads to identification of its novel signaling synthase (cneI), cognate receptor (cneR) and an orphan receptor

Tan KH, Tan JY, Yin WF, Chan KG

PeerJ, 2015;3:e1216.

PMID: 26355540 DOI: 10.7717/peerj.1216

Cedecea neteri is a very rare human pathogen. We have isolated a strain of C. neteri SSMD04 from pickled mackerel sashimi identified using molecular and phenotypics approaches. Using the biosensor Chromobacterium violaceum CV026, we have demonstrated the presence of short chain N-acyl-homoserine lactone (AHL) type quorum sensing (QS) activity in C. neteri SSMD04. Triple quadrupole LC/MS analysis revealed that C. neteri SSMD04 produced short chain N-butyryl-homoserine lactone (C4-HSL). With the available genome information of C. neteri SSMD04, we went on to analyse and identified a pair of luxI/R homologues in this genome that share the highest similarity with croI/R homologues from Citrobacter rodentium. The AHL synthase, which we named cneI(636 bp), was found in the genome sequences of C. neteri SSMD04. At a distance of 8bp from cneI is a sequence encoding a hypothetical protein, potentially the cognate receptor, a luxR homologue which we named it as cneR. Analysis of this protein amino acid sequence reveals two signature domains, the autoinducer-binding domain and the C-terminal effector which is typical characteristic of luxR. In addition, we found that this genome harboured an orphan luxR that is most closely related to easR in Enterobacter asburiae. To our knowledge, this is the first report on the AHL production activity in C. neteri, and the discovery of its luxI/R homologues, the orphan receptor and its whole genome sequence.

Fulltext Genome sequence analysis of multidrug-resistant Mycobacterium tuberculosis from Malaysia

Tan JL, Simbun A, Chan KG, Ngeow YF

Sci Data, 2020 05 05;7(1):135.

PMID: 32371951 DOI: 10.1038/s41597-020-0475-x

Mycobacterium tuberculosis (MTB) is commonly used as a model to study pathogenicity and multiple drug resistance in bacteria. These MTB characteristics are highly dependent on the evolution and phylogeography of the bacterium. In this paper, we describe 15 new genomes of multidrug-resistant MTB (MDRTB) from Malaysia. The assessments and annotations on the genome assemblies suggest that strain differences are due to lineages and horizontal gene transfer during the course of evolution. The genomes show mutations listed in current drug resistance databases and global MTB collections. This genome data will augment existing information available for comparative genomic studies to understand MTB drug resistance mechanisms and evolution.

Fulltext Genome sequence of Anoxybacillus ayderensis AB04(T) isolated from the Ayder hot spring in Turkey

Belduz AO, Canakci S, Chan KG, Kahar UM, Chan CS, Yaakop AS, et al.

Stand Genomic Sci, 2015;10:70.

PMID: 26413199 DOI: 10.1186/s40793-015-0065-2

Species of Anoxybacillus are thermophiles and, therefore, their enzymes are suitable for many biotechnological applications. Anoxybacillus ayderensis AB04(T) (= NCIMB 13972(T) = NCCB 100050(T)) was isolated from the Ayder hot spring in Rize, Turkey, and is one of the earliest described Anoxybacillus type strains. The present work reports the cellular features of A. ayderensis AB04(T), together with a high-quality draft genome sequence and its annotation. The genome is 2,832,347 bp long (74 contigs) and contains 2,895 protein-coding sequences and 103 RNA genes including 14 rRNAs, 88 tRNAs, and 1 tmRNA. Based on the genome annotation of strain AB04(T), we identified genes encoding various glycoside hydrolases that are important for carbohydrate-related industries, which we compared with those of other, sequenced Anoxybacillus spp. Insights into under-explored industrially applicable enzymes and the possible applications of strain AB04(T) were also described.

Fulltext Genome sequence of Dyella japonica strain A8, a quorum-quenching bacterium that degrades N-acylhomoserine lactones, isolated from Malaysian tropical soil

Chen JW, Chan KG

J Bacteriol, 2012 Nov;194(22):6331.

PMID: 23105069 DOI: 10.1128/JB.01637-12

Dyella japonica strain A8 is a Malaysian tropical soil bacterial strain which shows N-acylhomoserine lactone-degrading activity. Here, we present its draft genome sequence. A putative quorum-quenching gene was identified based on the genome sequence analysis of strain A8. To the best of our knowledge, this is the first genome announcement of a member from the genus of Dyella, and this is also the first work that reports the quorum-quenching activity of Dyella japonica.

Genome sequence of Roseivirga sp. strain D-25 and its potential applications from the genomic aspect

Selvaratnam C, Thevarajoo S, Ee R, Chan KG, Bennett JP, Goh KM, et al.

Mar Genomics, 2016 Apr 20.

PMID: 27107724 DOI: 10.1016/j.margen.2016.04.004

Roseivirga sp. strain D-25 is an aerobic marine bacterium isolated from seawater collected from Desaru beach, Malaysia. To date, the genus Roseivirga consists of only four species with no genome sequence reported. Here, we present the genome sequence of Roseivirga sp. strain D-25 (=KCTC 42709=DSM 101709), with a genome size of approximately 4.08Mbp and G+C content of 39.18%. Genome sequence analysis of strain D-25 revealed the presence of genes related to petroleum hydrocarbon degradation, 2,4,6-trinitrotoluene detoxification, heavy metals bioremediation and production of carotenoids, which shed light on the potential application of this strain.

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.

Fulltext Genome sequence of Streptomyces gilvigriseus MUSC 26T isolated from mangrove forest

Ser HL, Tan WS, Mutalib NA, Yin WF, Chan KG, Goh BH, et al.

Braz J Microbiol, 2018 02 02;49(2):207-209.

PMID: 29428207 DOI: 10.1016/j.bjm.2017.04.012

Streptomycetes remain as one of the important sources for bioactive products. Isolated from the mangrove forest, Streptomyces gilvigriseus MUSC 26T was previously characterised as a novel streptomycete. The high quality draft genome of MUSC 26T contained 5,213,277bp with G+C content of 73.0%. Through genome mining, several gene clusters associated with secondary metabolites production were revealed in the genome of MUSC 26T. These findings call for further investigations into the potential exploitation of the strain for production of pharmaceutically important compounds.

Displaying publications 161 - 180 of 370 in total