Displaying publications 1 - 20 of 319 in total

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  1. Detection and discrimination of Mycobacterium tuberculosis complex
    Issa R, Mohd Hassan NA, Abdul H, Hashim SH, Seradja VH, Abdul Sani A
    Diagn Microbiol Infect Dis, 2012 Jan;72(1):62-7.
    PMID: 22078904 DOI: 10.1016/j.diagmicrobio.2011.09.021
    A real-time quantitative polymerase chain reaction (qPCR) was developed for detection and discrimination of Mycobacterium tuberculosis (H37Rv and H37Ra) and M. bovis bacillus Calmette-Guérin (BCG) of the Mycobacterium tuberculosis complex (MTBC) from mycobacterial other than tuberculosis (MOTT). It was based on the melting curve (Tm) analysis of the gyrB gene using SYBR(®) Green I detection dye and the LightCycler 1.5 system. The optimal conditions for the assay were 0.25 μmol/L of primers with 3.1 mmol/L of MgCl(2) and 45 cycles of amplification. For M. tuberculosis (H37Rv and H37Ra) and M. bovis BCG of the MTBC, we detected the crossing points (Cp) at cycles of 16.96 ± 0.07, 18.02 ± 0.14, and 18.62 ± 0.09, respectively, while the Tm values were 90.19 ± 0.06 °C, 90.27 ± 0.09 °C, and 89.81 ± 0.04 °C, respectively. The assay was sensitive and rapid with a detection limit of 10 pg of the DNA template within 35 min. In this study, the Tm analysis of the qPCR assay was applied for the detection and discrimination of MTBC from MOTT.
    Matched MeSH terms: DNA, Bacterial/genetics
  2. Cloning of high activity xylanase gene from Bacillus pumilus PJ19
    Hamzah A, Abdulrashid N
    J. Biochem. Mol. Biol. Biophys., 2002 Oct;6(5):365-9.
    PMID: 12385974
    The xylanase gene from Bacillus pumilus PJ19 amplified by polymerase chain reaction (PCR) was cloned into pCRII vector and transformed into Escherichia coli strain INValphaF'. Starting from an ATG as an initiator codon, an open reading frame coding for 202 amino acids was obtained. The recombinant xylanase sequence showed a 96% homology with the xylanase sequence from B. pumilus IPO strain and had an estimated molecular weight of 22,474. Xylanase activity expressed by E. coli INValphaF' harboring the cloned gene was located primarily in the cytoplasmic fraction.
    Matched MeSH terms: DNA, Bacterial/genetics
  3. Fulltext Bacterial community in Haemaphysalis ticks of domesticated animals from the Orang Asli communities in Malaysia
    Khoo JJ, Chen F, Kho KL, Ahmad Shanizza AI, Lim FS, Tan KK, et al.
    Ticks Tick Borne Dis, 2016 07;7(5):929-937.
    PMID: 27132518 DOI: 10.1016/j.ttbdis.2016.04.013
    Ticks are vectors in the transmission of many important infectious diseases in human and animals. Ticks can be readily found in the semi-forested areas such as the settlements of the indigenous people in Malaysia, the Orang Asli. There is still minimal information available on the bacterial agents associated with ticks found in Malaysia. We performed a survey of the bacterial communities associated with ticks collected from domestic animals found in two Orang Asli villages in Malaysia. We collected 62 ticks, microscopically and molecularly identified as related to Haemaphysalis wellingtoni, Haemaphysalis hystricis and Haemaphysalis bispinosa. Bacterial 16s rRNA hypervariable region (V6) amplicon libraries prepared from the tick samples were sequenced on the Ion Torrent PGM platform. We detected a total of 392 possible bacterial genera after pooling and sequencing 20 samples, indicating a diverse bacterial community profile. Dominant taxa include the potential tick endosymbiont, Coxiella. Other dominant taxa include the tick-associated pathogen, Rickettsia, and environmental bacteria such as Bacillus, Mycobacterium, Sphingomonas and Pseudomonas. Other known tick-associated bacteria were also detected, including Anaplasma, Ehrlichia, Rickettsiella and Wolbachia, albeit at very low abundance. Specific PCR was performed on selected samples to identify Rickettsia and Coxiella. Sequence of Rickettsia felis, which causes spotted fever in human and cats, was identified in one sample. Coxiella endosymbionts were detected in three samples. This study provides the baseline knowledge of the microbiome of ticks in Malaysia, focusing on tick-associated bacteria affecting the Orang Asli communities. The role of the herein found Coxiella and Rickettsia in tick physiology or disease transmission merits further investigation.
    Matched MeSH terms: DNA, Bacterial/genetics
  4. Fulltext Utility of 16S rDNA Sequencing for Identification of Rare Pathogenic Bacteria
    Loong SK, Khor CS, Jafar FL, AbuBakar S
    J Clin Lab Anal, 2016 Nov;30(6):1056-1060.
    PMID: 27184222 DOI: 10.1002/jcla.21980
    BACKGROUND: Phenotypic identification systems are established methods for laboratory identification of bacteria causing human infections. Here, the utility of phenotypic identification systems was compared against 16S rDNA identification method on clinical isolates obtained during a 5-year study period, with special emphasis on isolates that gave unsatisfactory identification.

    METHODS: One hundred and eighty-seven clinical bacteria isolates were tested with commercial phenotypic identification systems and 16S rDNA sequencing. Isolate identities determined using phenotypic identification systems and 16S rDNA sequencing were compared for similarity at genus and species level, with 16S rDNA sequencing as the reference method.

    RESULTS: Phenotypic identification systems identified ~46% (86/187) of the isolates with identity similar to that identified using 16S rDNA sequencing. Approximately 39% (73/187) and ~15% (28/187) of the isolates showed different genus identity and could not be identified using the phenotypic identification systems, respectively. Both methods succeeded in determining the species identities of 55 isolates; however, only ~69% (38/55) of the isolates matched at species level. 16S rDNA sequencing could not determine the species of ~20% (37/187) of the isolates.

    CONCLUSION: The 16S rDNA sequencing is a useful method over the phenotypic identification systems for the identification of rare and difficult to identify bacteria species. The 16S rDNA sequencing method, however, does have limitation for species-level identification of some bacteria highlighting the need for better bacterial pathogen identification tools.

    Matched MeSH terms: DNA, Bacterial/genetics*
  5. Coxiella Detection in Ticks from Wildlife and Livestock in Malaysia
    Khoo JJ, Lim FS, Chen F, Phoon WH, Khor CS, Pike BL, et al.
    Vector Borne Zoonotic Dis, 2016 12;16(12):744-751.
    PMID: 27763821
    Recent studies have shown that ticks harbor Coxiella-like bacteria, which are potentially tick-specific endosymbionts. We recently described the detection of Coxiella-like bacteria and possibly Coxiella burnetii in ticks found from rural areas in Malaysia. In the present study, we collected ticks, including Haemaphysalis bispinosa, Haemaphysalis hystricis, Dermacentor compactus, Dermacentor steini, and Amblyomma sp. from wildlife and domesticated goats from four different locations in Malaysia. Coxiella 16s rRNA genomic sequences were detected by PCR in 89% of ticks tested. Similarity analysis and phylogenetic analyses of the 16s rRNA and rpoB partial sequences were performed for 10 representative samples selected based on the tick species, sex, and location. The findings here suggested the presence of C. burnetii in two samples, each from D. steini and H. hystricis. The sequences of both samples clustered with published C. burnetii sequences. The remaining eight tick samples were shown to harbor 16s rRNA sequences of Coxiella-like bacteria, which clustered phylogenetically according to the respective tick host species. The findings presented here added to the growing evidence of the association between Coxiella-like bacteria and ticks across species and geographical boundaries. The importance of C. burnetii found in ticks in Malaysia warrants further investigation.
    Matched MeSH terms: DNA, Bacterial/genetics
  6. Bacterial profiling of head lice isolated from the Orang Asli: A first report in Malaysia
    Abd Majid MA, Khoo JJ, Lim FS, Khor CS, Loong SK, Low VL, et al.
    Trop Biomed, 2020 Dec 01;37(4):884-895.
    PMID: 33612742 DOI: 10.47665/tb.37.4.884
    This study was carried out to determine from bacterial profiling to the bacterial profiles of head lice among the Orang Asli communities. The head lice were collected from Orang Asli community volunteers. The surface sterilized head lice pools were subjected to genomic DNA extraction while next generation sequencing of the 16S rRNA gene was performed using the Illumina MiSeq platform. Six female and three male head lice identified as Pediculus humanus capitis were collected. A total of 111 368 number of NGS sequencing reads were recorded while another 223 bacterial taxa sequences were obtained. Symbiotic bacteria showed the highest number of reads, with Arsenophonus and Rhodococcus sequences being the most abundant genera in the female and male samples, respectively. The female head lice contained a more distinct microbial diversity. Amongst the pathogenic bacterial species sequences noted were the methicillin-resistant Staphylococcus aureus, Streptobacillus moniliformis, Haemophilus influenzae, Bordetella pertussis and Acinetobacter baumannii. The 16S rRNA genome sequencing revealed a number of rare and pathogenic bacterial species within the head lice of the Orang Asli. The socio-economic practices of the community which involved forest foraging and hunting, and their poor living conditions potentially facilitated the transmission of zoonotic bacterial pathogens, including those found within the head lice. Hence, there is the possibility that the head lice could serve as vectors for the transmission of pathogenic bacteria. This study highlighted the diverse microbial community found within the head lice's gut of the Orang Asli, with the detection of multiple rare and pathogenic bacteria capable of causing severe infections.
    Matched MeSH terms: DNA, Bacterial/genetics
  7. Fulltext Genomic species identification of Acinetobacter of clinical isolates by 16S rDNA sequencing
    Misbah S, Hassan H, Yusof MY, Hanifah YA, AbuBakar S
    Singapore Med J, 2005 Sep;46(9):461-4.
    PMID: 16123830
    This study aims to identify Acinetobacter of clinical isolates from the University of Malaya Medical Centre (UMMC), Kuala Lumpur, to the species level by 16S rDNA sequencing.
    Matched MeSH terms: DNA, Bacterial/genetics*
  8. DNA markers for tuberculosis diagnosis
    Chin KL, Sarmiento ME, Norazmi MN, Acosta A
    Tuberculosis (Edinb), 2018 12;113:139-152.
    PMID: 30514496 DOI: 10.1016/j.tube.2018.09.008
    Tuberculosis (TB), caused by Mycobacterium tuberculosis complex (MTBC), is an infectious disease with more than 10.4 million cases and 1.7 million deaths reported worldwide in 2016. The classical methods for detection and differentiation of mycobacteria are: acid-fast microscopy (Ziehl-Neelsen staining), culture, and biochemical methods. However, the microbial phenotypic characterization is time-consuming and laborious. Thus, fast, easy, and sensitive nucleic acid amplification tests (NAATs) have been developed based on specific DNA markers, which are commercially available for TB diagnosis. Despite these developments, the disease remains uncontrollable. The identification and differentiation among MTBC members with the use of NAATs remains challenging due, among other factors, to the high degree of homology within the members and mutations, which hinders the identification of specific target sequences in the genome with potential impact in the diagnosis and treatment outcomes. In silico methods provide predictive identification of many new target genes/fragments/regions that can specifically be used to identify species/strains, which have not been fully explored. This review focused on DNA markers useful for MTBC detection, species identification and antibiotic resistance determination. The use of DNA targets with new technological approaches will help to develop NAATs applicable to all levels of the health system, mainly in low resource areas, which urgently need customized methods to their specific conditions.
    Matched MeSH terms: DNA, Bacterial/genetics*
  9. Distinct bacterial communities dominate tropical and temperate zone leaf litter
    Kim M, Kim WS, Tripathi BM, Adams J
    Microb Ecol, 2014 May;67(4):837-48.
    PMID: 24549745 DOI: 10.1007/s00248-014-0380-y
    Little is known of the bacterial community of tropical rainforest leaf litter and how it might differ from temperate forest leaf litter and from the soils underneath. We sampled leaf litter in a similarly advanced stage of decay, and for comparison, we also sampled the surface layer of soil, at three tropical forest sites in Malaysia and four temperate forest sites in South Korea. Illumina sequencing targeting partial bacterial 16S ribosomal ribonucleic acid (rRNA) gene revealed that the bacterial community composition of both temperate and tropical litter is quite distinct from the soils underneath. Litter in both temperate and tropical forest was dominated by Proteobacteria and Actinobacteria, while soil is dominated by Acidobacteria and, to a lesser extent, Proteobacteria. However, bacterial communities of temperate and tropical litter clustered separately from one another on an ordination. The soil bacterial community structures were also distinctive to each climatic zone, suggesting that there must be a climate-specific biogeographical pattern in bacterial community composition. The differences were also found in the level of diversity. The temperate litter has a higher operational taxonomic unit (OTU) diversity than the tropical litter, paralleling the trend in soil diversity. Overall, it is striking that the difference in community composition between the leaf litter and the soil a few centimeters underneath is about the same as that between leaf litter in tropical and temperate climates, thousands of kilometers apart. However, one substantial difference was that the leaf litter of two tropical forest sites, Meranti and Forest Research Institute Malaysia (FRIM), was overwhelmingly dominated by the single genus Burkholderia, at 37 and 23 % of reads, respectively. The 454 sequencing result showed that most Burkholderia species in tropical leaf litter belong to nonpathogenic "plant beneficial" lineages. The differences from the temperate zone in the bacterial community of tropical forest litter may be partly a product of its differing chemistry, although the unvarying climate might also play a role, as might interactions with other organisms such as fungi. The single genus Burkholderia may be seen as potentially playing a major role in decomposition and nutrient cycling in tropical forests, but apparently not in temperate forests.
    Matched MeSH terms: DNA, Bacterial/genetics
  10. Extensive Overlap of Tropical Rainforest Bacterial Endophytes between Soil, Plant Parts, and Plant Species
    Haruna E, Zin NM, Kerfahi D, Adams JM
    Microb Ecol, 2018 Jan;75(1):88-103.
    PMID: 28642991 DOI: 10.1007/s00248-017-1002-2
    The extent to which distinct bacterial endophyte communities occur between different plant organs and species is poorly known and has implications for bioprospecting efforts. Using the V3 region of the bacterial 16S ribosomal RNA (rRNA) gene, we investigated the diversity patterns of bacterial endophyte communities of three rainforest plant species, comparing leaf, stem, and root endophytes plus rhizosphere soil community. There was extensive overlap in bacterial communities between plant organs, between replicate plants of the same species, between plant species, and between plant organ and rhizosphere soil, with no consistent clustering by compartment or host plant species. The non-metric multidimensional scaling (NMDS) analysis highlighted an extensively overlapping bacterial community structure, and the β-nearest taxon index (βNTI) analysis revealed dominance of stochastic processes in community assembly, suggesting that bacterial endophyte operational taxonomic units (OTUs) were randomly distributed among plant species and organs and rhizosphere soil. Percentage turnover of OTUs within pairs of samples was similar both for plant individuals of the same species and of different species at around 80-90%. Our results suggest that sampling extra individuals, extra plant organs, extra species, or use of rhizosphere soil, might be about equally effective for obtaining new OTUs for culture. These observations suggest that the plant endophyte community may be much more diverse, but less predictable, than would be expected from culturing efforts alone.
    Matched MeSH terms: DNA, Bacterial/genetics
  11. Distinctive bacterial communities in the rhizoplane of four tropical tree species
    Oh YM, Kim M, Lee-Cruz L, Lai-Hoe A, Go R, Ainuddin N, et al.
    Microb Ecol, 2012 Nov;64(4):1018-27.
    PMID: 22767122 DOI: 10.1007/s00248-012-0082-2
    It is known that the microbial community of the rhizosphere is not only influenced by factors such as root exudates, phenology, and nutrient uptake but also by the plant species. However, studies of bacterial communities associated with tropical rainforest tree root surfaces, or rhizoplane, are lacking. Here, we analyzed the bacterial community of root surfaces of four species of native trees, Agathis borneensis, Dipterocarpus kerrii, Dyera costulata, and Gnetum gnemon, and nearby bulk soils, in a rainforest arboretum in Malaysia, using 454 pyrosequencing of the 16S rRNA gene. The rhizoplane bacterial communities for each of the four tree species sampled clustered separately from one another on an ordination, suggesting that these assemblages are linked to chemical and biological characteristics of the host or possibly to the mycorrhizal fungi present. Bacterial communities of the rhizoplane had various similarities to surrounding bulk soils. Acidobacteria, Alphaproteobacteria, and Betaproteobacteria were dominant in rhizoplane communities and in bulk soils from the same depth (0-10 cm). In contrast, the relative abundance of certain bacterial lineages on the rhizoplane was different from that in bulk soils: Bacteroidetes and Betaproteobacteria, which are known as copiotrophs, were much more abundant in the rhizoplane in comparison to bulk soil. At the genus level, Burkholderia, Acidobacterium, Dyella, and Edaphobacter were more abundant in the rhizoplane. Burkholderia, which are known as both pathogens and mutualists of plants, were especially abundant on the rhizoplane of all tree species sampled. The Burkholderia species present included known mutualists of tropical crops and also known N fixers. The host-specific character of tropical tree rhizoplane bacterial communities may have implications for understanding nutrient cycling, recruitment, and structuring of tree species diversity in tropical forests. Such understanding may prove to be useful in both tropical forestry and conservation.
    Matched MeSH terms: DNA, Bacterial/genetics
  12. Spatial scaling effects on soil bacterial communities in Malaysian tropical forests
    Tripathi BM, Lee-Cruz L, Kim M, Singh D, Go R, Shukor NA, et al.
    Microb Ecol, 2014 Aug;68(2):247-58.
    PMID: 24658414
    Spatial scaling to some extent determines biodiversity patterns in larger organisms, but its role in microbial diversity patterns is much less understood. Some studies have shown that bacterial community similarity decreases with distance, whereas others do not support this. Here, we studied soil bacterial communities of tropical rainforest in Malaysia at two spatial scales: a local scale with samples spaced every 5 mover a 150-m transect, and a regional scale with samples 1 to 1,800 km apart. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1–V3 region was pyrosequenced using Roche/454 GS FLX Titanium platform. A ranked partial Mantel test showed a weak correlation between spatial distance and whole bacterial community dissimilarity, but only at the local scale. In contrast, environmental distance was highly correlated with community dissimilarity at both spatial scales,stressing the greater role of environmental variables rather than spatial distance in determining bacterial community variation at different spatial scales. Soil pH was the only environmental parameter that significantly explained the variance in bacterial community at the local scale, whereas total nitrogen and elevation were additional important factors at the regional scale.We obtained similar results at both scales when only the most abundant OTUs were analyzed. A variance partitioning analysis showed that environmental variables contributed more to bacterial community variation than spatial distance at both scales. In total, our results support a strong influence of the environment in determining bacterial community composition in the rainforests of Malaysia. However, it is possible that the remaining spatial distance effect is due to some of the myriad of other environmental factors which were not considered here, rather than dispersal limitation.
    Matched MeSH terms: DNA, Bacterial/genetics
  13. Rainforest Conversion to Rubber Plantation May Not Result in Lower Soil Diversity of Bacteria, Fungi, and Nematodes
    Kerfahi D, Tripathi BM, Dong K, Go R, Adams JM
    Microb Ecol, 2016 08;72(2):359-71.
    PMID: 27221090 DOI: 10.1007/s00248-016-0790-0
    Large areas of rainforest in Asia have been converted to plantations, with uncertain effects on soil biodiversity. Using standard metagenetic methods, we compared the soil biota of bacteria, fungi, and nematodes at three rainforest sites in Malaysia with two rubber plantation sites with similar soils and geology. We predicted the following: (1) that the rubber sites would have a lower α- and β-diversity than the rainforest sites, due to the monospecific canopy cover and intensive management with herbicides, pesticides, and fertilizers, and (2) that due to differences in the physical and biotic environment associated with cultivation, there would be distinct communities of bacteria, fungi, and nematodes. However, regarding (1), the results showed no consistent difference in α- and β-diversity of bacteria, fungi, or nematodes between rainforest and rubber plantation sites. It appears that conversion of rainforest to rubber plantations does not necessarily result in a decrease in diversity of soil biota. It may be that heterogeneity associated with the cultivation regimen compensates for loss of biotically imposed heterogeneity of the original rainforest. Regarding (2), as predicted there were statistically significant differences in community composition between rainforest and rubber plantation for bacteria, fungi, and nematodes. These differences could be related to a range of factors including light level, litter fall composition, pH, C and N, selecting a distinct set of soil taxa, and it is possible that this in itself would affect long-term soil function.
    Matched MeSH terms: DNA, Bacterial/genetics
  14. Fulltext Impact of logging and forest conversion to oil palm plantations on soil bacterial communities in Borneo
    Lee-Cruz L, Edwards DP, Tripathi BM, Adams JM
    Appl Environ Microbiol, 2013 Dec;79(23):7290-7.
    PMID: 24056463 DOI: 10.1128/AEM.02541-13
    Tropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.
    Matched MeSH terms: DNA, Bacterial/genetics
  15. Fulltext Coxiella-like bacteria in fowl ticks from Thailand
    Trinachartvanit W, Maneewong S, Kaenkan W, Usananan P, Baimai V, Ahantarig A
    Parasit Vectors, 2018 Dec 27;11(1):670.
    PMID: 30587229 DOI: 10.1186/s13071-018-3259-9
    BACKGROUND: Coxiella bacteria were identified from various tick species across the world. Q fever is a zoonotic disease caused by the bacteria Coxiella burnetii that most commonly infects a variety of mammals. Non-mammalian hosts, such as birds, have also been reported to be infected with the pathogenic form of "Candidatus Coxiella avium". This research increases the list of tick species that have been found with Coxiella-like bacteria in Thailand.

    METHODS: A total of 69 ticks were collected from 27 domestic fowl (Gallus gallus domesticus), 2 jungle fowl (Gallus gallus) and 3 Siamese firebacks (Lophura diardi) at 10 locations (provinces) in Thailand. Ticks were identified and PCR was used to amplify Coxiella bacteria 16S rRNA, groEL and rpoB genes from the extracted tick DNA. MEGA6 was used to construct phylogenetic trees via a Maximum Likelihood method.

    RESULTS: The phylogenetic analysis based on the 16S rRNA gene showed that the Coxiella sequences detected in this study grouped in the same clade with Coxiella sequences from the same tick genus (or species) reported previously. In contrast, rpoB gene of the Coxiella bacteria detected in this study did not cluster together with the same tick genus reported previously. Instead, they clustered by geographical distribution (Thai cluster and Malaysian cluster). In addition, phylogenetic analysis of the groEL gene (the chaperonin family) showed that all Coxiella bacteria found in this study were grouped in the same clade (three sister groups).

    CONCLUSIONS: To our knowledge, we found for the first time rpoB genes of Coxiella-like bacteria in Haemaphysalis wellingtoni ticks forming two distinct clades by phylogenetic analysis. This may be indicative of a horizontal gene transfer event.

    Matched MeSH terms: DNA, Bacterial/genetics
  16. An ultrasensitive hollow-silica-based biosensor for pathogenic Escherichia coli DNA detection
    Ariffin EY, Lee YH, Futra D, Tan LL, Karim NHA, Ibrahim NNN, et al.
    Anal Bioanal Chem, 2018 Mar;410(9):2363-2375.
    PMID: 29504083 DOI: 10.1007/s00216-018-0893-1
    A novel electrochemical DNA biosensor for ultrasensitive and selective quantitation of Escherichia coli DNA based on aminated hollow silica spheres (HSiSs) has been successfully developed. The HSiSs were synthesized with facile sonication and heating techniques. The HSiSs have an inner and an outer surface for DNA immobilization sites after they have been functionalized with 3-aminopropyltriethoxysilane. From field emission scanning electron microscopy images, the presence of pores was confirmed in the functionalized HSiSs. Furthermore, Brunauer-Emmett-Teller (BET) analysis indicated that the HSiSs have four times more surface area than silica spheres that have no pores. These aminated HSiSs were deposited onto a screen-printed carbon paste electrode containing a layer of gold nanoparticles (AuNPs) to form a AuNP/HSiS hybrid sensor membrane matrix. Aminated DNA probes were grafted onto the AuNP/HSiS-modified screen-printed electrode via imine covalent bonds with use of glutaraldehyde cross-linker. The DNA hybridization reaction was studied by differential pulse voltammetry using an anthraquinone redox intercalator as the electroactive DNA hybridization label. The DNA biosensor demonstrated a linear response over a wide target sequence concentration range of 1.0×10-12-1.0×10-2 μM, with a low detection limit of 8.17×10-14 μM (R2 = 0.99). The improved performance of the DNA biosensor appeared to be due to the hollow structure and rough surface morphology of the hollow silica particles, which greatly increased the total binding surface area for high DNA loading capacity. The HSiSs also facilitated molecule diffusion through the silica hollow structure, and substantially improved the overall DNA hybridization assay. Graphical abstract Step-by-step DNA biosensor fabrication based on aminated hollow silica spheres.
    Matched MeSH terms: DNA, Bacterial/genetics
  17. Fulltext Identification of Brucella spp. isolated from human brucellosis in Malaysia using high-resolution melt (HRM) analysis
    Mohamed Zahidi J, Bee Yong T, Hashim R, Mohd Noor A, Hamzah SH, Ahmad N
    Diagn Microbiol Infect Dis, 2015 Apr;81(4):227-33.
    PMID: 25641125 DOI: 10.1016/j.diagmicrobio.2014.12.012
    Molecular approaches have been investigated to overcome difficulties in identification and differentiation of Brucella spp. using conventional phenotypic methods. In this study, high-resolution melt (HRM) analysis was used for rapid identification and differentiation of members of Brucella genus. A total of 41 Brucella spp. isolates from human brucellosis were subjected to HRM analysis using 4 sets of primers, which identified 40 isolates as Brucella melitensis and 1 as Brucella canis. The technique utilized low DNA concentration and was highly reproducible. The assay is shown to be a useful diagnostic tool, which can rapidly differentiate Brucella up to species level.
    Matched MeSH terms: DNA, Bacterial/genetics
  18. Fulltext Antibiotic susceptibility profile of Haemophilus influenzae and transfer of co-trimoxazole resistance determinants
    Mohd-Zain Z, Kamsani NH, Ismail IS, Ahmad N
    Trop Biomed, 2012 Sep;29(3):372-80.
    PMID: 23018500 MyJurnal
    Prior to the implementation of Haemophilus influenzae type b vaccination worldwide, H. influenzae has been one of the main causative agents of community acquired pneumonia and meningitis in children. Due to the lack of information on the characteristics of the H. influenzae isolates that have previously been collected in Malaysia, the H. influenzae were assessed of their microbial susceptibility to commonly used antibiotics. Emphasis was made on strains that were resistance to co-trimoxazole (SXT) and their mode of transfer of the antibiotic resistance determinants were examined. A collection of 34 H. influenzae isolates was serotyped and antimicrobial susceptibility tests were performed to 11 antibiotics. To the isolates that were found to be resistant to co-trimoxazole, minimum inhibition concentration (MIC) to SXT was performed using Etest while agar dilution method was used to measure the individual MICs of trimethoprim (TMP) and sulfamethoxazole (SUL). These isolates were also examined for presence of plasmid by PCR and isolation method. Conjugal transfers of SXT-resistant genes to SXT-susceptible hosts were performed to determine their rate of transfer. Result showed that 20.6% of the total number of isolates was serotype B while the remaining was non-typeable. Antimicrobial susceptibility profile of all the isolates revealed that 58.8% was resistant to at least one antibiotic. Majority of these isolates were equally resistant to ampicillin and tetracycline (29.4% each), followed by resistance to SXT (26.5%). From nine isolates that were found to be SXT-resistant, five contained plasmid/s. Conjugal transfer experiment showed that these five isolates with plasmid transferred SXT-resistance determinants at a higher frequency than those without. From these observations, it is postulated that plasmid is not involved in the transfer of SXT-resistance genes but presence of plasmid facilitates their transfer. The information obtained from this study provides some basic knowledge on the antimicrobial susceptibility pattern of the H. influenzae isolates and their mode of transfer of SXT-resistance genes.
    Matched MeSH terms: DNA, Bacterial/genetics
  19. Chryseobacterium artocarpi sp. nov., isolated from the rhizosphere soil of Artocarpus integer
    Venil CK, Nordin N, Zakaria ZA, Ahmad WA
    Int J Syst Evol Microbiol, 2014 Sep;64(Pt 9):3153-9.
    PMID: 24958763 DOI: 10.1099/ijs.0.063594-0
    A bacterial strain, designated UTM-3(T), isolated from the rhizosphere soil of Artocarpus integer (cempedak) in Malaysia was studied to determine its taxonomic position. Cells were Gram-stain-negative, non-spore-forming rods, devoid of flagella and gliding motility, that formed yellow-pigmented colonies on nutrient agar and contained MK-6 as the predominant menaquinone. Comparative analysis of the 16S rRNA gene sequence of strain UTM-3(T) with those of the most closely related species showed that the strain constituted a distinct phyletic line within the genus Chryseobacterium with the highest sequence similarities to Chryseobacterium lactis NCTC 11390(T), Chryseobacterium viscerum 687B-08(T), Chryseobacterium tructae 1084-08(T), Chryseobacterium arthrosphaerae CC-VM-7(T), Chryseobacterium oncorhynchi 701B-08(T), Chryseobacterium vietnamense GIMN1.005(T), Chryseobacterium bernardetii NCTC 13530(T), Chryseobacterium nakagawai NCTC 13529(T), Chryseobacterium gallinarum LMG 27808(T), Chryseobacterium culicis R4-1A(T), Chryseobacterium flavum CW-E2(T), Chryseobacterium aquifrigidense CW9(T), Chryseobacterium ureilyticum CCUG 52546(T), Chryseobacterium indologenes NBRC 14944(T), Chryseobacterium gleum CCUG 14555(T), Chryseobacterium jejuense JS17-8(T), Chryseobacterium oranimense H8(T) and Chryseobacterium joostei LMG 18212(T). The major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c, followed by summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7t) and iso-C17 : 0 3-OH, and the polar lipid profile consisted of phosphatidylethanolamine and several unknown lipids. The DNA G+C content strain UTM-3(T) was 34.8 mol%. On the basis of the phenotypic and phylogenetic evidence, it is concluded that the isolate represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium artocarpi sp. nov. is proposed. The type strain is UTM-3(T) ( = CECT 8497(T) = KCTC 32509(T)).
    Matched MeSH terms: DNA, Bacterial/genetics
  20. Molecular identification of ticks infesting camels and the detection of their natural infections with Rickettsia and Borrelia in Riyadh province, Saudi Arabia
    Alajmi RA, Ayaad TH, Al-Harbi HT, Shaurub EH, Al-Musawi ZM
    Trop Biomed, 2019 Sep 01;36(3):758-765.
    PMID: 33597497
    The present work aimed to identify camel ticks Hyalomma dromedarii and Hyalomma marginatum using direct sequence of the mitochondrial 16S rRNA gene and the detection of their natural infection rate with Rickettsia and Borrelia using the PCR/ hybridization method for amplification of the citrate synthase (gltA) gene. The phylogenetic analysis showed 99% similarity between Hyalomma dromedarii and its reference with accession # L34306.1, as well as between Hyalomma marginatum and its reference with accession # KT391060.1 obtained from GenBank data base. The prevalence of H. dromedarii and H. marginatum was about 99% and 1%, respectively. The intraspecific variation among H. dromedarii ranged between 0.2-6.6%. The interspecific variation between H. dromedarii and H. marginatum was 18.3%. PCR/hybridization of the sampled H. dromedarii detected about 31%, 37% and 18% natural infection with Rickettsia, Borrelia and co-infection with both pathogens, respectively. In contrast, none of Rickettsia or Borrelia was detected in H. marginatum. The present study emphasizes the accuracy of the identification of camel ticks based on molecular techniques. The ability of H. dromedarii to spread more than one disease is an important issue from the epidemiological standpoint. Future epidemiological research should be carried out in Saudi Arabia to monitor the distribution of tick species and suggest effective control strategies.
    Matched MeSH terms: DNA, Bacterial/genetics
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