Currrent Issue: Volume 3, Number 3, 2015


The Evaluation on Molecular Techniques of Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP), Reverse Transcription Polymerase Chain Reaction (RT-PCR), and Their Diagnostic Results on MinIONTM Nanopore Sequencer for the Detection of Dengue Virus Serotypes

1Department of Clinical Pathology, Faculty of Medicine, Sam Ratulagi University, Manado, Indonesia

2Department of Physiology, Faculty of Medicine, University of Hasanuddin, Makassar, Indonesia

3Department of Parasitology, Faculty of Medicine, University of Hasanuddin, Makassar, Indonesia.

4Molecular Biology and Immunology Laboratory, Department of Microbiology, Faculty of Medicine, University of Hasanuddin, Makassar, Indonesia

American Journal of Microbiological Research. 2015, 3(3), 118-124
doi: 10.12691/ajmr-3-3-4
Copyright © 2015 Science and Education Publishing

Cite this paper:
Arthur Elia Mongan, Irawan Yusuf, Isra Wahid, Mochammad Hatta. The Evaluation on Molecular Techniques of Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP), Reverse Transcription Polymerase Chain Reaction (RT-PCR), and Their Diagnostic Results on MinIONTM Nanopore Sequencer for the Detection of Dengue Virus Serotypes. American Journal of Microbiological Research. 2015; 3(3):118-124. doi: 10.12691/ajmr-3-3-4.

Correspondence to: Mochammad  Hatta, Molecular Biology and Immunology Laboratory, Department of Microbiology, Faculty of Medicine, University of Hasanuddin, Makassar, Indonesia. Email:


Background and aims:. Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Assay is a method described as a simple, rapid, and cost-effective, and a powerful gene amplification technique for rapid identification of microbial infection. The aims of this study were to validate a reverse-transcription LAMP method (RT-LAMP) with a reverse-transcription PCR technique (RT-PCR) for DENV serotype detection, and to evaluate the potential of this RT-LAMP method from which its amplification product can be applied for MinIONTM Nanopore sequencing. Methods: This study was performed by using 26 patient serum samples from the Confirmed group and 23 sera from the Suspected group, and 10 sera from Healthy volunteer group. The same validation study to confirm the sensitivity and specificity between the RT-LAMP assay and RT-PCR was also conducted by making a serial dilution of template as well as dengue serotype detected sera. Furthermore, experiments of MinIONTM Nanopore sequencer using the amplification product (amplicon) of RT-LAMP assay from patient serum samples and its comparative diagnostics with RT-PCR and Sanger’s Sequencing were also done. Results: From the validation study, 17 (65.4%) out of the 26 sera of Confirmed group were serotype detected by RT-LAMP assay, compared to that of RT-PCR which was only 10 (38.4%). Same result in Suspected group, there were 11 (47.8%) out of 23 sera of Suspected group were serotype detected by RT-LAMP assay, compared to that of RT-PCR which was only 1 (4.3%). For the Healthy group, the result was somewhat comparable between the two methods. In the serial dilution study, RT-LAMP was superior than that of the RT-PCR technique, particularly seen in the serial dilution of clinical serum samples. The limit of detection of RT-LAMP was down to the titer of 1/1000x, while RT-PCR was only 1/10x. Secondly, amplicon of RT-LAMP assay from patient serum samples fits to be sequenced by the MinIONTM. In the comparative study, the results showed that RT-LAMP was more sensitive and specific compared to that of the RT-PCR technique and Sanger’s Sequencing. Conclusions: RT-LAMP assay was more sensitive to that of RT-PCR technique. In the comparative study using MinIONTM Nanopore sequencer for the detection of dengue virus serotypes, the RT-LAMP was more sensitive and specific to that of RT-PCR and Sanger’s Sequencing. The method of RT-LAMP should be applied more because its sensitive and specific, simple, rapid, cost-effective, and also can be a tool of point of care testing for the detection of dengue virus serotypes.



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Microbial and Parasitic Contamination on Vegetables Collected From Retailers in Main Market, Akure, Nigeria

1Department of Microbiology, The Federal University of Technology, Akure, Nigeria

American Journal of Microbiological Research. 2015, 3(3), 112-117
doi: 10.12691/ajmr-3-3-3
Copyright © 2015 Science and Education Publishing

Cite this paper:
Dada E. O., Olusola-Makinde O. O.. Microbial and Parasitic Contamination on Vegetables Collected From Retailers in Main Market, Akure, Nigeria. American Journal of Microbiological Research. 2015; 3(3):112-117. doi: 10.12691/ajmr-3-3-3.

Correspondence to: Olusola-Makinde  O. O., Department of Microbiology, The Federal University of Technology, Akure, Nigeria. Email:


Laboratory investigations were carried out on six different vegetable samples; Amaranthus cruentus (Amaranth), Talinum triangulare (Waterleaf), Solanecio biafrae (Worowo), Brassica olerecea (Cabbage), Lactuca sativa (Lettuce) and Daucus carota (Carrot) purchased from retailers in main market, Akure, Nigeria to determine the microbial and parasitic contamination. One part of each sample was washed with distilled water while the other part was washed with physiological saline. For parasitological analysis, the solutions were centrifuged, decanted and viewed under the microscope while culturing was done for microbial analysis using the pour plate technique. Only L. sativa was contaminated with helminth; Ascaris lumbricoides. All samples were found to be populated with various species of microorganisms. Seven bacteria belonging to different genera and six fungi were isolated randomly and identified from the vegetables. Bacteria include Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, Serratia marcescens, Salmonella typii and Proteus vulgaris while fungi are Aspergillus niger, Saccharomyces sp, Penicillium sp, Rhizopus stolonifer, Fusarium sp and Mucor mucedo. The total bacterial count ranged from 3.2×106 to 7.2 ×106cfu/g for samples washed with distilled water and 1.6 x 106 to 4.8×106cfu/g for samples washed with physiological saline. S. aureus had the highest occurrence of 25% while Salmonella typhii had the least occurrence of 10%. The fungal count ranged from 3.0×105 to 5.0×105sfu/g for samples washed with distilled water and 1.0×105 to 3.0×105sfu/g for samples washed with physiological saline. R. stolonifer had the highest percentage of occurrence of 33.3%. Saccharomyces had the occurrence of 22.2% and Penicillium sp, A. niger, Mucor mucedo, Fusarium sp had the least occurrence of 11.1%. This study showed the presence of organisms of health significance on retail vegetables. Reduction of risk of human illness associated with raw produce can be achieved through controlling points of potential contamination.



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Molecular Study of Panton-Valentine Leukocidin Genes among Staphylococcus aureus Clinical Isolates in Khartoum State, Sudan

1Department of Biotechnology, Faculty of Science and Technology, Omdurman Islamic University, Sudan

2College of Applied Medical Science, Shaqra University, KSA

3Department of Microbiology, Tropical Medicine Research Institute, National Center for Research, Sudan

4Department of Microbiology, Faculty of Medicine, King Khalid University, KSA

5Department of Biotechnology, Biotechnology Park, Africa City of Technology, Sudan

American Journal of Microbiological Research. 2015, 3(3), 107-111
doi: 10.12691/ajmr-3-3-2
Copyright © 2015 Science and Education Publishing

Cite this paper:
Najem Aldin M. Osman, Intisar E. Alrayah, Yassir Mahgoub Mohamed, Ali M El-Eragi, Muataz M. Eldirdery, Mohamed Ahmed Salih. Molecular Study of Panton-Valentine Leukocidin Genes among Staphylococcus aureus Clinical Isolates in Khartoum State, Sudan. American Journal of Microbiological Research. 2015; 3(3):107-111. doi: 10.12691/ajmr-3-3-2.

Correspondence to: Najem  Aldin M. Osman, Department of Biotechnology, Faculty of Science and Technology, Omdurman Islamic University, Sudan. Email:


Staphylococcus aureus strains carrying Panton- Valentine Leukocidin genes (PVL) are an emerging threat worldwide, causing variety of infections even in healthy individuals. Intensive efforts through the last years have been carried out towards the detection and analysis of PVL genes. The prevalence and characterization of such genes has not been done in Sudan. In this study we investigated the prevalence and the molecular characteristics of PVL genes among S. aureus clinical isolates, comparing their PVL allelic variant with that of PVL positive strains from different countries. Standard microbiological procedures were used for the identification of isolates, polymerase chain reaction for determination of PVL genes and standard sequencing for mapping of lukS/F-PV genes. In Silico tools were used for sequence analysis. Among 210 S. aureus isolates, PVL genes were detected in 122 (58%). Sequence analysis for lukS/F-PV genes from 12 representative isolates detected a new point mutation in lukS PV region. Collectively, our findings showed a high frequency of PVL genes among S. aureus isolates and revealed a novel nonsynonymous mutation. Phylogenetic analysis revealed that Sudanese isolates were closely related to each other.



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Removal of Heavy Metals from Aqueous Solutions Using Multi-Metals and Antibiotics Resistant Bacterium Isolated from the Red Sea, Egypt

1Botany Department, Faculty of Science, Menoufia University, Egypt

2Marine Microbiology Laboratory, National Institute of Oceanography and Fisheries, Egypt

3Marine Pollution Laboratory, National Institute of Oceanography and Fisheries, Egypt

American Journal of Microbiological Research. 2015, 3(3), 93-106
doi: 10.12691/ajmr-3-3-1
Copyright © 2015 Science and Education Publishing

Cite this paper:
Mohamed T. Shaaban, Hassan A.H. Ibrahim, Ahmed S. Abouhend, Khalid M. El-Moselhy. Removal of Heavy Metals from Aqueous Solutions Using Multi-Metals and Antibiotics Resistant Bacterium Isolated from the Red Sea, Egypt. American Journal of Microbiological Research. 2015; 3(3):93-106. doi: 10.12691/ajmr-3-3-1.

Correspondence to: Ahmed  S. Abouhend, Marine Pollution Laboratory, National Institute of Oceanography and Fisheries, Egypt. Email:,


This investigation was incorporate screening for the highest multiple metal and antibiotics resistant marine bacteria at the Northern Red Sea. The two selected bacterial isolates were identified on the basis of phenotypic and genotypic characterization through 16S rDNA gene technique as Alteromonas macleodii and Nitratireductor basaltis. A. macleodii revealed high efficiency in the removal of heavy metals from aqueous solution. Different factors influenced the removal of heavy metals from aqueous solution by A. macleodii such salinity, pH, temperature, biomass and contact time were optimized. The metal removal was greater at the lowest initial metal concentration (50 mg l-1) and decreased with increase in the metal concentration. A. macleodii showed high efficiency in biosorption of different metals in single and multiple metal solution systems. Removal percentage of different metals by A. macleadii in a single metal system at the highest tested metal concentrations (200 mg l-1) reached Pb, 73.8%; Mn, 66%; Fe, 65%; Cu, 64%; Zn, 62%; Ni, 54%; and Cd, 53%. In multiple metal systems containing 30 mg l-1 of different metals, biosorption percentage was Pb, 93%; Fe, 89%; Zn, 55%; Cd, 50%; Cu, 44.5%; Mn, 40% and Ni, 36%. These findings suggest the possibility of using these bacterial isolates for bioremediation of heavy metals from heavy metal contaminated ecosystem.



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