Microbial Genomics

Ecotoxicological Evaluations of Saw-Milling Activities

Human Health Risks Perception and In Situ Ecotoxicological Evaluations of Saw-Milling Activities on the Lagos lagoon, Nigeria Using Tilapia and Blue Crab


1*Sogbanmu, T.  O. and 2Ogunkoya, O. A.

1,2Ecotoxicology and Conservation Unit, Department of Zoology, Faculty of Science, University of Lagos, Akoka 101017, Lagos, Nigeria.

*Participating/Corresponding Author Email: tsogbanmu@unilag.edu.ng



The Okobaba waterfront of the Lagos lagoon, Lagos, Nigeria is exposed to several forms of pollution as a result of wastes generated and discharged from saw-milling activities around the area. The aim of the study was to evaluate the human health risks perception and biological effects of these saw-milling activities on aquatic organisms in the lagoon. The methods utilised for the study were administration of structured human health risks questionnaires to 200 stakeholders in the area, physico-chemical analyses of water and sediment samples as well as in situ toxicity studies to evaluate biochemical and histological effects in Tilapia guineensis (Guinean Tilapia) and Callinectes amnicola (Blue Crab) deployed at the test site over a period of 28 days. The results revealed that saw dusts contribute to 84% of the wastes, 92% of which is burnt and run-off into the lagoon, air quality is highly impacted by the saw-milling activities, symptoms often experienced by respondents were headaches (53%) and skin irritations (28%). Most of the physico-chemical parameters were higher than set limits. Polycyclic aromatic hydrocarbons (PAHs) levels in water and sediments at the test site were significantly different (p<0.05) from the control site. In situ studies showed significant differences (p<0.05) in the concentrations of antioxidant enzymes in the liver and gills of Tilapia guineensis after 28 days compared to control. Histological alterations were observed in the liver cells of T. guineensis only over the study period. The results demonstrate the perception of human health risks by stakeholders working and living around the test site particularly due to the poor air quality from the burning activities and the adverse effects of the saw-mill activities on sensitive fish like T. guineensis. We recommend further empirical studies on the molecular basis and mechanisms of toxicity in exposed animals and humans using genomics tools.


Keywords: Biomarkers, in situ studies, Lagos lagoon, Human health risks perception, Tilapia guineensis, Callinectes amnicola



KATG Gene in Isoniazid Resistant M.Tb



Gusai H. Abdel Samad1, Solima M. A. Sabeel2,*, Walaa A. Abuelgassim3, Abeer E. Abdelltif 3,4, Wisam M. Osman3,Mona A. Haroun5, Somaya M. Soliman6, Sami. A. B. Salam1, Hamid. A. Hamdan7, Mohamed A. Hassan 3,8,9.


1 Department of Microbiology, university of Bahri, Sudan

2 Department of Microbiology,Faculty of Medical Laboratory Sciences, Ibn Sina University, Sudan

3 Department of Bioinformatics, Africa City of Technology, Sudan

4 Department of Computer Sciences, Najran University, KSA

5 Department of Histopathology, ALzaim AL-Azhari University, Sudan

6 Department of Microbiology Al borg Medical Laboratories, UAE

7 Department of environmental Health, University of Hail, KSA

8 Division of Molecular Genetics, University of Tuebingen, Germany 9University, HNO –universities Klink-Tuebingen (Germany)


*Corresponding author



Aims: To detect mutation(s) within KatG that responsible for converting MTB to INH resistance and to investigate the predicted protein’s stability. 

Background: Tuberculosis (TB) remains a major health problem caused by Mycobacterium tuberculosis (MTB) bacteria. It is infect approximately 10 million people annually according to WHO global TB report 2017. Isoniazid (INH) is a prodrug that activated by catalase peroxidase enzyme coded by KatG gene. It was considered as main chemotherapy used throughout the world to manage TB, therefore resistance of INH occur in strains with impaired KatG gene.

Methods: A total of 305 Mycobacterium tuberculosis strains from Abu-Anja hospital for chest disease were obtained and identified by conventional biochemical tests.  Genomic DNA were extracted, katG gene were amplified by PCR. Consecutive isolates (n = 20) of KatG gene hot regions were sequenced and analyzed through bioinformatics tool such as BLAST to check sequence similarity, BioEdit for sequence alignment, GeneMark S to  translate DNA sequence into amino acids, i-mutant to estimate protein stability, Chimera to predict the tertiary model of protein and phylogeny.fr to draw phylogenetic tree.

Results: 70% (14/20) of sequences revealed 100% identity with EGY-K361 strain retrieved from database with Accession No: KC49137 while 30% (6/20) revealed 99% of similarity in BLAST. BioEdit illustrate transversion from guanine in to cytosine that convert serine (SER) at codon 315 in to Threonine (THR). Stability of mutant protein was increased. On phylogenetic tree most of mutant strains accumulate in one subgroup except one strain reported as the out-group sequence.

Conclusion: In silico tools have great impact to understand genetic variation. The substitution changed efficiency of INH, therefore S315T could be used as rapid screening marker to diagnosis INH resistant for more effective treatment prescription.





Tayseer Qasim1* and Faisal Hammad Mekky Koua1,2*

1Department of Biochemistry & Molecular Biology, Faculty of Science & Technology, Al Neelain University, El-Baladiya Ave, PO Box 12702, Khartoum, Sudan. 2National University Research Institute-NURI, National University, Air St, PO Box 3783, Khartoum, Sudan.

*Email: Tyseer114@hotmail.com

Haram Mohammed2 ,Department of Biology & Biotechnology Faculty of Science & Technology Al Neelain University ,El Baladiya Ave  PO Box 12702 Khartoum Sudan.

Tipyan Omer Mahgoub3, Department of Biology & Biotechnology Faculty of Science & Technology Al Neelain University, El Baladiya Ave  PO Box 12702 Khartoum Sudan.

Background and aim: pink-pigmented facultative methylotrophic (PPFM) bacteria are a group of heterotrophs that are characterized by their ability to metabolize C1 compound, and to the distinctive pigmentation owing to the carotenoids rendering them to be tolerant to radiation and high light intensities. Most methylotrophs are beneficial to plant and human health, however, some have been reported to be pathogen to human. Nonetheless, little is known about the mechanisms of these methylotrophs with their environments as well as their responses to the different biotic and abiotic stresses in terms of secreted peptides/proteins and metabolites, i.e. secretome and metabolome, respectively. Methods: in the present study, nine cultivable water methylotrophic isolates from the Nile river; G1 (A12, A11, B32, B12N), G2 (A11N, B31, A12N), G3 (A22) and G4 (B11N), were identified using conventional microbiological methods. Comprehensive phylogenetic analysis to the mxaF and xoxF genes of the methanol dehydrogenase as well as the 16S rDNA gene were used in comparison with 30 reported PPFM. Results: G1, G3, G3 and G4 were successfully identified as Moraxella kingii, Cardiobacterium hominis, Pasteurella haemolytica type T, p. trehalosi and Pasteurella haemolytica type T, p. haemolytica, respectively, and further tested for their resistance to antibiotics. 16S rDNA sequencing as well as a total genome sequencing using Illumina next-generation sequencing will be considered. The response of these strains to antibiotics, inter-species interactions with other microorganism and heavy metals will be evaluated focusing on the secretome and extracellular metabolome. Conclusion: all together, the present study will provide novel information regarding methylotrophy and the role of abiotic stresses in enhancing or diminishing the methylotrophic metabolism in these PPFMs.



Metagenomic analysis – Mycetoma

Metagenomic analysis of Environmental samples from Mycetoma endemic area in Sudan


Sahar Mubarak Bakhiet 1 , Abdalla Ahmed3  , Najwa A. Mhmoud 2, Emmanuel Edwar Siddig 2 Lamis Yahia Mohamed 4 , Ahmed Mudawi Musa 1, Ahmed Hassan Fahal 2

1 Institute of Endemic Diseases, University of Khartoum, Sudan.

2 The Mycetoma Research Centre, University of Khartoum, Khartoum, Sudan

3 Umm Al-Qura University, MAKKAH, Saudi Arabia

4 Faculty of Pharmacy-University of Khartoum


Background: Mycetoma is a unique neglected tropical disease caused by a considerable number of microorganisms of fungal or bacterial origins and characterized by devastating deformities, disabilities and high morbidity. Studies to date suggest a soil-borne or thorn-prick-mediated origin of mycetoma infections suggesting an environmental role in the disease transmission.

Study objective: To identify and characterize the different Madurella species communities from soils, thorns, water and other environmental samples collected from Sennar State, Sudan using ITS rRNA genes sequencing.

Methods: This cross sectional study was conducted at Eastern Sennar Governate , Sudan in 2016. A total of 105 environmental specimens were collected form mycetoma endemic villages. Environmental samples were including soil, thorns, animal dung and others. DNA was extracted from all environmental samples and pooled into 18 pools according to the similarity of ecological niches. The Internal Transcribed Spacer 2 of the ribosomal DNA were enriched by PCR for sequencing and the libraries were sequenced using Illumina MiSeq. The sequence reads were checked for quality using FastQC and directly mapped to a database containing reference ITS2 sequences of Madurella mycetomatis, Madurella pseudomycetomatis, Madurella tropicana and Madurella fahalii. Additionally, the sequence reads from different samples’ pools were denovo assembled using SeqMan NGen and the assembled contigs were used for BLAST search in Unite Database.

Results: Madurella mycetomatis was found in 6 environmental samples’ pools. In these 6 positive samples, Madurella pseudomycetomatis or/and Madurella tropicana were also detected. Madurella fahalii was found in only one pool co-existing with all other Madurella species. Madurella mycetomatis and Madurella fahalii were co-detected in two different contigs in the assembled reads from only one samples’ pool. Conclusion: Madurella mycetomatis was found to be more common than other Madurella species in this highly endemic area. The use of direct mapping of raw sequence reads is more sensitive in the detection of Madurella species in metagenomics environmental specimens.



Genetic Susceptibility to Mycetoma


Rayan S. Ali1,3, Sahar Mubarak Bakhiet1,2*, Ahmed Hassan Fahal1, Muntaser E Ibrahim2, Melanie Newport3

1 The Mycetoma Research Centre, University of Khartoum, Khartoum, Sudan.

2 Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.

3 Brighton and Sussex Medical School, Brighton, UK.

*Corresponding author: Dr. Sahar Mubarak Bakhiet, Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, 11111 Khartoum, Sudan. P.O. box 102. email: saharbakhiet@iend.org



Mycetoma is a neglected tropical disease affecting disadvantaged communities in tropical regions.  Although exact prevalence data are not available, Sudan has one of the highest burdens of disease globally.  The condition typically occurs following traumatic inoculation of the causative organism into the subcutaneous tissue but it is notable that not all individuals exposed to infection develop clinical disease.  It is likely that there are multiple factors that contribute to this observation including those attributable to the environment and to the pathogen. There is also evidence that host factors may be important.


The aim of this study is to specifically investigate the role of host genetic factors in susceptibility to mycetoma.


DNA samples were collected from members of two families with multiple cases of mycetoma who live in Sinnar state (one of the highly endemic areas).  DNA samples from 10 members of these families, representing a mix of affected and unaffected family members from both sexes was sent for whole exome sequencing (WES). WES and variant calling were both done by BGI® (Hong Kong, China). 

WES variant prioritization and filtering was done based on the variants’ impact and their effect of on protein structure, function or expression. ClinVar database and Varsome impact analysis tool were used to detect variants related to clinical conditions.


WES variant analysis revealed functional variants in 3 candidate genes.  To confirm the functionality of these variants, real-time PCR (RT-PCR) is now being performed to detect difference in gene expression, of the three candidate genes, between eumycetoma patients and healthy controls.


Based on the findings of this pilot study, we aim to expand the mycetoma genetics resources to the already established Mycetoma Research Centre (MRC) biobank to be used for family based WES and heritability estimation, and population based association studies.





Gene Diversity of Immunoglobulin


Ahmed Rahaman A., Adekoya Khalid and Okoli Victoria

Medical Genetics Unit, Cell Biology and Genetics Department, University of Lagos, Nigeria

 Identification of vaccine-compatible antibodies capable of eliciting absolute protection against HIV infection is a global quest. Africa representation in the antibody gene databases is however low and may have implications in the global development of a quality and efficient HIV vaccine. Sequencing of immunoglobulin heavy chain variable domain (IGHV) was performed on 28 HIV infected subjects in Zulu ethnic group of South Africa, 123 novel alleles were identified and at least 8 were functional against HIV infection. This suggests that novel functional immunoglobulin gene variants are embedded in Africa population. We therefore want to explore antibody gene diversity in Nigeria being the largest population in Africa and with diverse heterogeneous ethnic groups. Illumina MiSeq will be used to sequence the entire rearranged antigen naïve variable chain gene repertoires in 105 subjects from three major ethnic groups of Nigeria; Yoruba, Hausa and Igbo. IgDiscover bioinformatics tool will be used to identify novel and known germline variable and joining antibody gene segments. Expected outcome of this extended study includes identification of large and diverse alleles, bulk of which may be missing in the public immunoglobulin databases. Novel alleles will further be assessed for functional HIV antigenic responses. This study will contribute to general knowledge of antibody especially towards utilization for a quality HIV vaccine development and other infectious diseases. It will also be of great importance to the Antibodyomics project which is aimed to provide holistic and cross-sectional information on human antibodies especially against HIV infection.

Presenter: Mr. Rahaman Ademolu Ademolu

Medical Genetics Unit, Cell Biology and Genetics Department, University of Lagos, Nigeria


Vaccine Against Onchocerciasis



Robert Adamu Shey1,3, Ntang Emmaculate1, Yaah Esoh Kum Kevin2, Neba Derrick Nebangwa1, Shintouo Cabirou Mounchili1, Nkemngo Francis Nongley4, Fru Asa Bertha5, Ferdinand Ngale Njume1,3, Stephen Mbigha Ghogomu1,, Jacob Souopgui3,+

1Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Cameroon.

2Department of Biochemistry, Faculty of Science, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya.

3Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM Universite Libre de Bruxelles, Gosselies Campus, Belgium.

4Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Cameroon

5Department of Public Health and Hygiene, Faculty of Health Science, University of Buea, Cameroon

Onchocerciasis is a neglected tropical disease with enormous socio-economic burden. The disease caused by the parasite Onchocerca volvulus is transmitted by Simulium blackflies. It is the second leading cause of infectious blindness, with over 99% of 15.5 million cases occurring in Africa. The plan of elimination by 2025 in 80% of African countries is hampered by many obstacles including reports of parasite resistance to ivermectin and the serious challenges to development of new drugs. A suitable vaccine has been proposed as a way to circumvent control limitations in control measures. With the presence of the genomes and proteomes of the parasite, more efficacious vaccines can be developed. 
A multi-epitope prophylactic/therapeutic vaccine targeting the parasite infective L3 and microfilaria stages is invaluable for onchocerciasis elimination since these two stages are respectively responsible for infection and disease pathology. An immuno-informatics approach was applied to design a multi-epitope subunit vaccine construct consisting B-and T-cell epitopes of vaccinogenic proteins obtained from immunomic studies.  Docking of the validated 3D structure of the chimera with TLR4 predicted efficient binding. Immune simulation predicted high levels of IgG1, T-helper, T-cytotoxic cells, INF-γ and IL-2 responses. Overall, the chimera demonstrated superior antigenicity to the current vaccine candidate leads and could be a vital tool in onchocerciasis elimination programs.




Mustafa E Yassin1, Khalid A Enan2, Bashir Salim3, Walid A Eldaif1, Imad Fadl-Elmula4, Isam M Elkhidir6

Authors Affiliation

1Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Alneelain University, Khartoum, Sudan

2Department of Virology, Central Laboratory, Ministry of science and Communication, P.O. Box 7099, Khartoum, Sudan.

3Parasites, Vectors and Vector-Borne Diseases, Agricultural Research Council-Onderstepoort Veterinary Institute, Onderstepoort 0110, South Africa

4Faculty of Medicine, Al Neelain University, Khartoum, Sudan.

5Department of Medical Microbiology and Parasitology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan


Aim: This study was conducted to evaluate RT-LAMP method for HIV-1 detection in comparison with RT-PCR.

Background: Rapid, simple, cost effective, nucleic acid based test for detecting HIV-1 in areas with limited resources is badly needed. Loop-mediated isothermal amplification (LAMP) is a technique that allows the amplification of nucleic acids DNA and RNA with high specificity, sensitivity and rapidity under isothermal conditions.

Methods: In the present study, ninety EDTA blood samples were studied; seventy samples were collected from HIV-1 infected patients and 20 samples from HIV-1 negative participants. All samples subjected to RT-LAMP and RT-PCR assay targeting HIV-1 p24 gene. Additionally nine positive samples were subjected to viral load measurement using COBAS® TaqMan® HIV-1 Test, version 2.0 (v2.0), and five samples were subjected to direct DNA sequencing of p24 gene phylogenetic analysis. Results: Of the 70 HIV-1 positive samples, 68 (97.1%) and 61 (87.1%) positive samples were detected using RT-LAMP and RT-PCR respectively. Whereas, all the 20 HIV-1 negative samples were confirmed negative by RT-LAMP, 2 (10%) were positive by RT-PCR. Furthermore, the limit of detection (LOD) for both RT-LAMP and RT-PCR assays was determined to be 130 and 325 copies/ml respectively. The viral loads for the nine samples ranged between 1.92E+4C/ml – 1.04C6/ml. The sequencing of five samples showed similarity of the Sudanese isolates with the neighboring countries Uganda, Saudi Arabia and also Senegal and even more closely sub-grouped with the Tanzanian counterpart.

Conclusion: RT-LAMP was successfully performed under minimal laboratory conditions demonstrating it as a very useful for use in fields setting and limited resources region.

Keywords: RT-LAMP, RT-PCR, HIV, Sudan, COBAS TaqMan, Phylogeny.


Dr. MUSTAFA ELTIGANI MUSTAFA YASSIN, Assistant professor of Medical Microbiology.

Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Alneelain University, Khartoum, Sudan



Next Generation Sequencing

Next Generation Sequencing Provides Comparable Data to Sanger Sequencing for the Detection of HIV Protease Inhibitor Mutations


Mukhlid Yousif1,2, Sergio Carmona3,4, Johanna Ledwaba1, Kim Steegen3,4, Lynn Morris1,2 and Gillian Hunt1,2

National Institute for Communicable Diseases, Centre for HIV and STI, Johannesburg, South

Africa1, University of the Witwatersrand, Virology, Johannesburg, South Africa2, University of the Witwatersrand, Molecular Medicine and Haematology, Johannesburg, South Africa3, National Health Laboratory Service, Johannesburg, South Africa4



South African national guidelines recommend HIV drug resistance (HIVDR) testing for all HIV-infected patients failing a protease inhibitor (PI) based regimen. Currently, Sanger sequencing is used for HIVDR testing, however the implementation of next generation sequencing (NGS) could improve sensitivity, reduce cost and increase specimen throughput. The aims of this study were to compare Sanger and Illumina NGS methods for their ability to detect PI drug resistance mutations among patients failing a PI regimen. A total of 162 specimens with PI mutations detected by Sanger sequencing were selected for this study. A 1.7kb fragment spanning protease and reverse transcriptase genes was amplified using an in-house PCR assay. Library preparation was performed using a Nextera XT kit. Paired-end libraries were indexed in a single MiSeq run (96 specimens) and sequenced using MiSeq Reagent kit V3. FastQ files were analysed using DeepChek®. A consensus sequence was generated for each specimen to compare with Sanger sequences. The validation process of the NGS and Sanger sequences was done successfully using phylogenetic analysis and pairwise analysis. Using a 15% cut-off for generating a consensus sequence, 155/162 (95.7%) of specimens showed similar HIVdb resistance mutation scores between Sanger and NGS, while 7 specimens (4.3%) showed discordance between the two techniques. When using 5-15% consensus cut-off, an additional 13 specimens (8%) showed discordance. In conclusions, detection of DRMs using MiSeq and Sanger sequencing showed high concordance (95.7%). The difference in the HIVdb resistance mutation scores was due to discrepancies in mutations detected. The discrepancies had minor impact on clinical interpretation as all scores were >15 for LPV/r and ATZ/r, which is the cut-off for switching patients to 3rd line therapy. The use of NGS for HIVDR testing is therefore reliable and allows for large specimen numbers to be tested in a more efficient workflow.


Drug Resistant Genes of M.Tuberculosis

Detection of Drug-Resistant Genes of Mycobacterium tuberculosis in Sudanese Tuberculosis Patients in Khartoum State Using Multiplex PCR

Mohammed Saad Mohammed Farah Alnour 1,2, Abdel Rhim Mohammed Elhussein 3, Isam

Mohammed Elkhidir 4, Seif Eldin Tayeib 5, Osama Mohammed Khair 6, Nouh S Mohamed 7,8,9 and Khalid A Enan 6 *

1 Microbiology Department, El-Zaiam El Azahari University, Sudan

2 Molecular Biology Department, Institute Of Endemic Diseases, Khartoum University, Sudan

3 Central Laboratory, Ministry Of Science and Technology, Khartoum, Sudan

4 Virology Department, Faculty of Medicine, University of Khartoum, Khartoum, Sudan

5 Omdourman Teaching Hospital, Abu Anga for Pulmonary Diseases Unit.

6 Virology Department, Central Laboratory, Ministry Of Science and Technology

7 Parasitology and Medical Entomology, Sinnar University, Sudan

8 Molecular Biology, National University Research Institute, National University, Sudan

9 Parasitology and Medical Entomology, Nile College, Sudan


*Corresponding Author: Khalid A Enan, Virology Department, Central Laboratory, Ministry Of Science and Technology.


Background: Tuberculosis is a common contiguous disease caused by M. tuberculosis. With an estimated 9 million new cases and 2 million deaths every year, tuberculosis represents one of the most serious infectious diseases worldwide. The increased death rate is a result of emergence of new strains of M. tuberculosis resistant to some or all current anti-tubercular drugs. The resistance is attributed primarily to improper prescriptions or patient noncompliance.

Aim: In this study we aimed to detect the frequency of drug resistance genes (rpoB, katG and pncA) in Sudanese tuberculosis patients.

Method: Seventy sputum samples were collected from Omdurman Teaching Hospital (Abu Anga) in Khartoum state, Sudan. Sputum samples were disinfected and then DNA was extracted. Multiplex PCR was used to detect drug resistance genes (rpoB, katG and pncA). IS6110 gene was used to confirm the presence of M. tuberculosis in the tested samples. Results: Fifty six sputum samples out of 70 were positive for the presence of drug resistance genes, drug resistance genes were detected in 22 (41.3%) for rifampicin, 29 (41.4%) for isoniazid and 33 (47.1%) for Pyrazinamide, also 16 (28.6%) samples had mono drug resistance, 29 (51.8%) had multi drug resistance and 11 (19.6%) had poly drug resistance. The ability of M. tuberculosis for the development of drug resistant gene were found to be associated with many factors, however in this study hypertension and diabetes mellitus were of no significant in the contribution of developing drug resistance P. Value > 0.574.

Conclusion: This study provides the first data about Pyrazinamide, isoniazid and rifampicin resistance in Sudan using multiplex PCR. Also representing that multiplex PCR assay use is a rapid, reliable tool and easy to perform for the routine detection of resistant M. tuberculosis strains in TB positive patients in Sudan.

Keywords: Mycobacterium tuberculosis; Rifampicin; Isoniazid; Pyrazinamide; Multidrug Resistance