MyMedR

Whole-genome sequencing in the prediction of antimicrobial resistance

Chan KG

Expert Rev Anti Infect Ther, 2016 07;14(7):617-9.

PMID: 27215476 DOI: 10.1080/14787210.2016.1193005

Fulltext Whole-genome sequence of N-acylhomoserine lactone-synthesizing and -degrading Acinetobacter sp. strain GG2

Hong KW, Koh CL, Sam CK, Yin WF, Chan KG

J Bacteriol, 2012 Nov;194(22):6318.

Acinetobacter sp. strain GG2 is a quorum-sensing and quorum-quenching bacterium isolated from the ginger rhizosphere. It degrades a broad range of N-acylhomoserine lactone molecules via lactonase. The genome sequence of strain GG2 may provide insights on the regulation of quorum-sensing and quorum-quenching mechanisms in this bacterium.

Fulltext Whole-genome sequence of Enterobacter sp. strain SST3, an endophyte isolated from Jamaican sugarcane (Saccharum sp.) stalk tissue

Gan HM, McGroty SE, Chew TH, Chan KG, Buckley LJ, Savka MA, et al.

J Bacteriol, 2012 Nov;194(21):5981-2.

PMID: 23045495 DOI: 10.1128/JB.01469-12

Enterobacter sp. strain SST3 is an endophytic bacterium isolated from Saccharum spp. Here we present its annotated draft genome that may shed light on its role as a bacterial endophyte of sugarcane. To our knowledge, this is the first genome announcement of a sugarcane-associated bacterium from the genus Enterobacter.

Fulltext Whole-genome sequence of Cupriavidus sp. strain BIS7, a heavy-metal-resistant bacterium

Hong KW, Thinagaran Da, Gan HM, Yin WF, Chan KG

J Bacteriol, 2012 Nov;194(22):6324.

PMID: 23115161 DOI: 10.1128/JB.01608-12

Cupriavidus sp. strain BIS7 is a Malaysian tropical soil bacterium that exhibits broad heavy-metal resistance [Co(II), Zn(II), Ni(II), Se(IV), Cu(II), chromate, Co(III), Fe(II), and Fe(III)]. It is particularly resistant to Fe(II), Fe(III), and Zn(II). Here we present the assembly and annotation of its genome.

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.

Fulltext Whole-Genome Sequencing Analysis of Quorum-Sensing Aeromonas hydrophila Strain M023 from Freshwater

Tan WS, Yin WF, Chang CY, Chan KG

Genome Announc, 2015;3(1).

PMID: 25700404 DOI: 10.1128/genomeA.01548-14

Aeromonas hydrophila is a well-known waterborne pathogen that recently was found to infect humans. Here, we report the draft genome of a freshwater isolate from a Malaysian waterfall, A. hydrophila strain M023, which portrays N-acylhomoserine lactone-dependent quorum sensing.

Fulltext Whole-Genome Sequencing Analysis of Chromobacterium piscinae Strain ND17, a Quorum-Sensing Bacterium

Chan KG, Yunos NY

Genome Announc, 2016;4(2).

PMID: 26941152 DOI: 10.1128/genomeA.00081-16

Here, we report the draft genome sequence of Chromobacterium piscinae strain ND17. This bacterium was isolated from a fresh water sample in Malaysia and exhibits quorum-sensing activity. This first draft genome of C. piscinae strain ND17 will pave the way to future studies of the quorum-sensing properties of this isolate.

Fulltext Whole-Genome Sequence of Stenotrophomonas maltophilia ZBG7B Reveals Its Biotechnological Potential

Chan KG, Chong TM, Adrian TG, Kher HL, Hong KW, Grandclément C, et al.

Genome Announc, 2015;3(6).

PMID: 26659682 DOI: 10.1128/genomeA.01442-15

Stenotrophomonas maltophilia ZBG7B was isolated from vineyard soil of Zellenberg, France. Here, we present the draft genome sequence of this bacterial strain, which has facilitated the prediction of function for several genes encoding biotechnologically important enzymes, such as xylosidase, xylanase, laccase, and chitinase.

Fulltext Whole-Genome Sequence of Quorum-Sensing Vibrio tubiashii Strain T33

Izzati Mohamad N, Yin WF, Chan KG

Genome Announc, 2015;3(1).

PMID: 25555738 DOI: 10.1128/genomeA.01362-14

Vibrio tubiashii strain T33 was isolated from the coastal waters of Morib, Malaysia, and was shown to possess quorum-sensing activity similar to that of its famous relative Vibrio fischeri. Here, the assembly and annotation of its genome are presented.

Fulltext Whole-Genome Sequence and Fosfomycin Resistance of Bacillus sp. Strain G3(2015) Isolated from Seawater off the Coast of Malaysia

Chan XY, Chen JW, Adrian TG, Hong KW, Chang CY, Yin WF, et al.

Genome Announc, 2017 Mar 30;5(13).

PMID: 28360153 DOI: 10.1128/genomeA.00067-17

Bacillus sp. is a Gram-positive bacterium that is commonly found in seawater. In this study, the genome of marine Bacillus sp. strain G3(2015) was sequenced using MiSeq. The fosfomycin resistant gene fosB was identified upon bacterial genome annotation.

Fulltext Whole-Genome Phylogenetic Analysis of Influenza B/Phuket/3073/2013-Like Viruses and Unique Reassortants Detected in Malaysia between 2012 and 2014

Oong XY, Ng KT, Tan JL, Chan KG, Kamarulzaman A, Chan YF, et al.

PLoS One, 2017;12(1):e0170610.

PMID: 28129386 DOI: 10.1371/journal.pone.0170610

Reassortment of genetic segments between and within influenza B lineages (Victoria and Yamagata) has been shown to generate novel reassortants with unique genetic characteristics. Based on hemagglutinin (HA) and neuraminidase (NA) genes, recent surveillance study has identified reassortment properties in B/Phuket/3073/2013-like virus, which is currently used in the WHO-recommended influenza vaccine. To understand the potential reassortment patterns for all gene segments, four B/Phuket/3073/2013-like viruses and two unique reassortants (one each from Yamagata and Victoria) detected in Malaysia from 2012-2014 were subjected to whole-genome sequencing. Each gene was phylogenetically classified into lineages, clades and sub-clades. Three B/Phuket/3073/2013-like viruses from Yamagata lineage were found to be intra-clade reassortants, possessing PA and NA genes derived from Stockholm/12-like sub-clade, while the remaining genes from Wisconsin/01-like sub-clade (both sub-clades were within Yamagata Clade 3/Yam-3). However, the other B/Phuket/3073/2013-like virus had NS gene that derived from Stockholm/12-like sub-clade instead of Wisconsin/01-like sub-clade. One inter-clade reassortant had Yamagata Clade 2/Yam-2-derived HA and NP, and its remaining genes were Yam-3-derived. Within Victoria Clade 1/Vic-1 in Victoria lineage, one virus had intra-clade reassortment properties: HA and PB2 from Vic-1B sub-clade, MP and NS from a unique sub-clade "Vic-1C", and the remaining genes from Vic-1A sub-clade. Although random reassortment event may generate unique reassortants, detailed phylogenetic classification of gene segments showed possible genetic linkage between PA and NA genes in B/Phuket/3073/2013-like viruses, which requires further investigation. Understanding on reassortment patterns in influenza B evolution may contribute to future vaccine design.

Fulltext Whole-Genome Analysis of Quorum-Sensing Burkholderia sp. Strain A9

Chan KG, Chen JW, Tee KK, Chang CY, Yin WF, Chan XY

Genome Announc, 2015;3(2).

PMID: 25745000 DOI: 10.1128/genomeA.00063-15

Burkholderia spp. rely on N-acyl homoserine lactone as quorum-sensing signal molecules which coordinate their phenotype at the population level. In this work, we present the whole genome of Burkholderia sp. strain A9, which enables the discovery of its N-acyl homoserine lactone synthase gene.

Fulltext Whole-Genome Analysis of Aeromonas hydrophila Strain 187, Exhibiting Quorum-Sensing Activity

Chan XY, Chua KH, Yin WF, Puthucheary SD, Chan KG

Genome Announc, 2014;2(6).

PMID: 25540357 DOI: 10.1128/genomeA.01360-14

Aeromonas hydrophila is a quorum-sensing (QS) bacterium that causes diarrhea in humans upon infection. Here, we report the genome of pathogenic Aeromonas hydrophila strain 187, which possesses a QS gene responsible for signaling molecule N-acyl homoserine lactone (AHL) synthesis and has been found to be located at contig 36.

Fulltext Whole genome sequencing enables the characterization of BurI, a LuxI homologue of Burkholderia cepacia strain GG4

How KY, Hong KW, Chan KG

PeerJ, 2015;3:e1117.

PMID: 26290785 DOI: 10.7717/peerj.1117

Quorum sensing is a mechanism for regulating proteobacterial gene expression in response to changes in cell population. In proteobacteria, N-acyl homoserine lactone (AHL) appears to be the most widely used signalling molecules in mediating, among others, the production of extracellular virulence factors for survival. In this work, the genome of B. cepacia strain GG4, a plasmid-free strain capable of AHL synthesis was explored. In silico analysis of the 6.6 Mb complete genome revealed the presence of a LuxI homologue which correspond to Type I quorum sensing. Here, we report the molecular cloning and characterization of this LuxI homologue, designated as BurI. This 609 bp gene was cloned and overexpressed in Escherichia coli BL21(DE3). The purified protein was approximately 25 kDa and is highly similar to several autoinducer proteins of the LuxI family among Burkholderia species. To verify the AHL synthesis activity of this protein, high resolution liquid chromatography-mass spectrometry analysis revealed the production of 3-oxo-hexanoylhomoserine lactone, N-octanoylhomoserine lactone and 3-hydroxy-octanoylhomoserine lactone from induced E. coli BL21 harboring the recombinant BurI. Our data show, for the first time, the cloning and characterization of the LuxI homologue from B. cepacia strain GG4 and confirmation of its AHL synthesis activity.

Fulltext Whole genome analysis of Klebsiella pneumoniae T2-1-1 from human oral cavity

Chan KG, Yin WF, Chan XY

Genom Data, 2016 Mar;7:105-6.

PMID: 26981378 DOI: 10.1016/j.gdata.2015.12.008

Klebsiella pneumoniae T2-1-1 was isolated from the human tongue debris and subjected to whole genome sequencing on HiSeq platform and annotated on RAST. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession JAQL00000000.

Vitellibacter aquimaris sp. nov., a marine bacterium isolated from seawater

Thevarajoo S, Selvaratnam C, Goh KM, Hong KW, Chan XY, Chan KG, et al.

Int J Syst Evol Microbiol, 2016 Sep;66(9):3662-3668.

PMID: 27334651 DOI: 10.1099/ijsem.0.001248

A Gram-staining-negative, aerobic, yellow-orange-pigmented, rod-shaped bacterium designated D-24T was isolated from seawater from sandy shoreline in Johor, Malaysia. The 16S rRNA gene sequence analysis revealed that strain D-24T is affiliated with the genus Vitellibacter. It shared more than 96 % sequence similarity with the types of some of the validly published species of the genus: Vitellibactervladivostokensis KMM 3516T (99.5 %), Vitellibactersoesokkakensis RSSK-12T (97.3 %), VitellibacterechinoideorumCC-CZW007T (96.9 %), VitellibacternionensisVBW088T (96.7 %) and Vitellibacteraestuarii JCM 15496T (96.3 %). DNA-DNA hybridization and genome-based analysis of average nucleotide identity (ANI) of strain D-24T versus V.vladivostokensisKMM 3516T exhibited values of 35.9±0.14 % and 89.26 %, respectively. Strain D-24T showed an even lower ANI value of 80.88 % with V. soesokkakensis RSSK-12T. The major menaquinone of strain D-24T was MK-6, and the predominant fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. Strain D-24T contained major amounts of phosphatidylethanolamine, two lipids and two aminolipids, and a phosphoglycolipid that was different to that of other species of the genus Vitellibacter. The genomic DNA G+C content was 40.6 mol%. On the basis of phenotypic properties, DNA-DNA relatedness, ANI value and chemotaxonomic analyses, strain D-24T represents a novel species of the genus Vitellibacter, for which the name Vitellibacter aquimaris sp. nov. is proposed. The type strain is D-24T (=KCTC 42708T=DSM 101732T).

Viral Load and Sequence Analysis Reveal the Symptom Severity, Diversity, and Transmission Clusters of Rhinovirus Infections

Ng KT, Oong XY, Lim SH, Chook JB, Takebe Y, Chan YF, et al.

Clin Infect Dis, 2018 07 02;67(2):261-268.

PMID: 29385423 DOI: 10.1093/cid/ciy063

Background: Rhinovirus (RV) is one of the main viral etiologic agents of acute respiratory illnesses. Despite the heightened disease burden caused by RV, the viral factors that increase the severity of RV infection, the transmission pattern, and seasonality of RV infections remain unclear.

Methods: An observational study was conducted among 3935 patients presenting with acute upper respiratory illnesses in the ambulatory settings between 2012 and 2014.

Results: The VP4/VP2 gene was genotyped from all 976 RV-positive specimens, where the predominance of RV-A (49%) was observed, followed by RV-C (38%) and RV-B (13%). A significant regression in median nasopharyngeal viral load (VL) (P < .001) was observed, from 883 viral copies/µL at 1-2 days after symptom onset to 312 viral copies/µL at 3-4 days and 158 viral copies/µL at 5-7 days, before declining to 35 viral copies/µL at ≥8 days. In comparison with RV-A (median VL, 217 copies/µL) and RV-B (median VL, 275 copies/µL), RV-C-infected subjects produced higher VL (505 copies/µL; P < .001). Importantly, higher RV VL (median, 348 copies/µL) was associated with more severe respiratory symptoms (Total Symptom Severity Score ≥17, P = .017). A total of 83 phylogenetic-based transmission clusters were identified in the population. It was observed that the relative humidity was the strongest environmental predictor of RV seasonality in the tropical climate.

Conclusions: Our findings underline the role of VL in increasing disease severity attributed to RV-C infection, and unravel the factors that fuel the population transmission dynamics of RV.

Fulltext Vibrio vulnificus: An Environmental and Clinical Burden

Heng SP, Letchumanan V, Deng CY, Ab Mutalib NS, Khan TM, Chuah LH, et al.

Front Microbiol, 2017;8:997.

PMID: 28620366 DOI: 10.3389/fmicb.2017.00997

Vibrio vulnificus is a Gram negative, rod shaped bacterium that belongs to the family Vibrionaceae. It is a deadly, opportunistic human pathogen which is responsible for the majority of seafood-associated deaths worldwide. V. vulnificus infection can be fatal as it may cause severe wound infections potentially requiring amputation or lead to sepsis in susceptible individuals. Treatment is increasingly challenging as V. vulnificus has begun to develop resistance against certain antibiotics due to their indiscriminate use. This article aims to provide insight into the antibiotic resistance of V. vulnificus in different parts of the world as well as an overall review of its clinical manifestations, treatment, and prevention. Understanding the organism's antibiotic resistance profile is vital in order to select appropriate treatment and initiate appropriate prevention measures to treat and control V. vulnificus infections, which should eventually help lower the mortality rate associated with this pathogen worldwide.

Fulltext Vibrio parahaemolyticus: a review on the pathogenesis, prevalence, and advance molecular identification techniques

Letchumanan V, Chan KG, Lee LH

Front Microbiol, 2014;5:705.

PMID: 25566219 DOI: 10.3389/fmicb.2014.00705

Vibrio parahaemolyticus is a Gram-negative halophilic bacterium that is found in estuarine, marine and coastal environments. V. parahaemolyticus is the leading causal agent of human acute gastroenteritis following the consumption of raw, undercooked, or mishandled marine products. In rare cases, V. parahaemolyticus causes wound infection, ear infection or septicaemia in individuals with pre-existing medical conditions. V. parahaemolyticus has two hemolysins virulence factors that are thermostable direct hemolysin (tdh)-a pore-forming protein that contributes to the invasiveness of the bacterium in humans, and TDH-related hemolysin (trh), which plays a similar role as tdh in the disease pathogenesis. In addition, the bacterium is also encodes for adhesions and type III secretion systems (T3SS1 and T3SS2) to ensure its survival in the environment. This review aims at discussing the V. parahaemolyticus growth and characteristics, pathogenesis, prevalence and advances in molecular identification techniques.

Vibrio coralliirubri sp. nov., a new species isolated from mucus of red coral (Corallium rubrum) collected at Procida island, Italy

Poli A, Romano I, Mastascusa V, Buono L, Orlando P, Nicolaus B, et al.

Antonie Van Leeuwenhoek, 2018 Jul;111(7):1105-1115.

PMID: 29299771 DOI: 10.1007/s10482-017-1013-5

Strain Corallo1T was isolated from mucus of red coral (Corallium rubrum) at Punta Pizzaco (Procida island, Naples, Italy). It was characterised as a Gram-stain negative, motile, rod-shaped bacterium. Strain Corallo1T was found to show positive responses for cytochrome-c oxidase, catalase, reduction of nitrate and nitrite, β-galactosidase activity and hydrolysis of starch, xylan, peptone, Tween 40, Tween 80 and casein. Strain Corallo1T was found to be mesophilic, neutrophilic to alkalophilic and slightly halophilic. According to analysis of the almost-complete 16S rRNA gene, strain Corallo1T is closely related to Vibrio celticus (100% sequence similarity), Vibrio gigantis (100%), Vibrio crassostreae (99.7%), Vibrio artabrorum (99.7%) and Vibrio pomeroyi (99.6%). MLSA of five housekeeping genes (atpA, pyrH, recA, rpoA and rpoD) was performed to refine the phylogenetic relationships of strain Corallo1T. A draft genome sequence of strain Corallo1T was obtained. The DNA G+C content of this strain was determined to be 44.5 mol %. The major cellular fatty acids of strain Corallo1T are C16:1, n-C16:0 and C18:1, and the major isoprenoid ubiquinone is Q8. ANI indexes, in silico estimations of DDH values and wet lab DDH values demonstrated that strain Corallo1T represents an independent genomospecies. Based on a polyphasic taxonomic characterisation, strain Corallo1T is concluded to represent a novel species of the genus Vibrio, for which the name Vibrio coralliirubri sp. nov. is proposed. The type strain is Corallo1T (= DSM 27495T = CIP 110630T).

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