Muzamil Abdel Hamid - Academia.edu (original) (raw)

Papers by Muzamil Abdel Hamid

Research paper thumbnail of ’ s response to reviews Title : Monoallelic Characteristic-Bearing Heterozygous L 1053 X in BRCA 2 Gene among Sudanese women with Breast Cancer

Research paper thumbnail of Prevalence of glucose-6-phosphate dehydrogenase deficiency (G6PDd), CareStart qualitative rapid diagnostic test performance, and genetic variants in two malaria-endemic areas in Sudan

PLOS Neglected Tropical Diseases

Glucose-6-phosphate dehydrogenase deficiency (G6PDd) is the most common enzymopathy globally, and... more Glucose-6-phosphate dehydrogenase deficiency (G6PDd) is the most common enzymopathy globally, and deficient individuals may experience severe hemolysis following treatment with 8-aminoquinolines. With increasing evidence of Plasmodium vivax infections throughout sub-Saharan Africa, there is a pressing need for population-level data at on the prevalence of G6PDd. Such evidence-based data will guide the expansion of primaquine and potentially tafenoquine for radical cure of P. vivax infections. This study aimed to quantify G6PDd prevalence in two geographically distinct areas in Sudan, and evaluating the performance of a qualitative CareStart rapid diagnostic test as a point-of-care test. Blood samples were analyzed from 491 unrelated healthy persons in two malaria-endemic sites in eastern and central Sudan. A pre-structured questionnaire was used which included demographic data, risk factors and treatment history. G6PD levels were measured using spectrophotometry (SPINREACT) and firs...

Research paper thumbnail of Abstracts of the Eighth EDCTP Forum, 6–9 November 2016

S OF PLENARY PRESENTATIONS A3 ABSTRACTS OF ORAL PRESENTATIONS A5S OF ORAL PRESENTATIONS A5 ABSTRA... more S OF PLENARY PRESENTATIONS A3 ABSTRACTS OF ORAL PRESENTATIONS A5S OF ORAL PRESENTATIONS A5 ABSTRACTS OF POSTER PRESENTATIONS A16S OF POSTER PRESENTATIONS A16

Research paper thumbnail of Invasive Malaria Vector Anopheles stephensi Mosquitoes in Sudan, 2016–2018

Emerging Infectious Diseases

Anopheles stephensi mosquitoes are urban malaria vectors in Asia that have recently invaded the H... more Anopheles stephensi mosquitoes are urban malaria vectors in Asia that have recently invaded the Horn of Africa. We detected emergence of An. stephensi mosquitoes in 2 noncontiguous states of eastern Sudan. Results of mitochondrial DNA sequencing suggest the possibility of distinct invasions, potentially from a neighboring country.

Research paper thumbnail of Socio-Ecological Systems Analysis and Health System Readiness in Responding to Dengue Epidemics in Ilala and Kinondoni Districts, Tanzania

Frontiers in Tropical Diseases

IntroductionSince 2010, Tanzania has been experiencing frequent outbreaks of dengue. The objectiv... more IntroductionSince 2010, Tanzania has been experiencing frequent outbreaks of dengue. The objectives of this study were to carry out a socio-ecological systems (SES) analysis to identify risk factors and interventions and assess the readiness of the district in the prevention and control of dengue.MethodsThe study utilized a cross-sectional purposive selection of key stakeholders responsible for disease surveillance and response in human and animal sectors in Ilala and Kinondoni districts in Tanzania. A SES framework was used to identify drivers and construct perceived thematic causal explanations of the dengue outbreaks in the study districts. A mapping exercise was carried out to analyse the performance of the disease surveillance system at district and facility levels. A semi-structured questionnaire was used to assess the districts’ readiness in the response to dengue outbreak.ResultsThe two districts were characterized by both urban and peri-urban ecosystems, with a mixture of p...

Research paper thumbnail of Socio-ecological Systems Analysis of the Prevention and Control of Dengue in two Districts of Dar es Salaam City, Tanzania

Background: Since 2010, Tanzania has been experiencing frequent outbreaks of dengue. The objectiv... more Background: Since 2010, Tanzania has been experiencing frequent outbreaks of dengue. The objective of this study was to carry out a socio-ecological systems analysis and assess the readiness in dengue prevention and control in Kinondoni and Ilala districts of Dar es Salaam City, Tanzania.Methods: Twenty-seven key district officials responsible for human and animal health were involved in a socio-ecological systems framework analysis as regards to dengue. In addition, the readiness of the districts to respond to dengue outbreaks and the performance of the disease surveillance system was assessed.Results: The two districts were characterized by both urban and peri-urban ecosystems, with a mixture of planned and unplanned settlements which support breeding and proliferation of Aedes mosquitoes. The results indicate inadequate levels of readiness in the management and control of dengue outbreaks, in terms of clinical competence, diagnostic capacities, surveillance system and control/pre...

Research paper thumbnail of Detection and characterization of carbapenem resistant Gram‐negative bacilli isolates recovered from hospitalized patients at Soba University Hospital, Sudan

BMC Microbiology

Background Antimicrobial resistance (AMR) poses a complex threat to global health security and un... more Background Antimicrobial resistance (AMR) poses a complex threat to global health security and universal health coverage. Recently, nosocomial infections with carbapenemase-producing Gram-negative bacilli (GNB) is increasing worldwide. We report the molecular characterization and detection of genes associated with carbapenemase producing Gram negative bacteria isolated from hospitalized patients at Soba University Hospital (SUH) in Khartoum State, Sudan. Results Between October 2016 and February 2017, a total of 206 GNB clinical specimens were collected from hospitalized patients in SUH. Of 206 carbapenem resistance isolates, 171 (83 %) were confirmed as phenotypically resistant and 121 (58.7 %) isolates harboured one or more carbapenemase genes. New Delhi metallo-β-lactamase (NDM) types were the most predominant genes, blaNDM 107(52 %), followed by blaIMP 7 (3.4 %), blaOXA-48 5(2.4 %) and blaVIM 2 (0.9 %). Co-resistance genes with NDM producing GNB were detected in 87 (81.3 %) of a...

Research paper thumbnail of Quantitative analysis of candidate endodontic pathogens and their association with cause and symptoms of apical periodontitis in a Sudanese population

European Endodontic Journal

Objective: To investigate the prevalence of key endodontic pathogens and their association with t... more Objective: To investigate the prevalence of key endodontic pathogens and their association with the clinical features and the cause of apical periodontitis. Methods: The study population included patients referred to Khartoum Dental teaching Hospital, Sudan for endodontic treatment. Samples were collected from single-rooted teeth carious or traumatised teeth with clinical and radiographic evidence of apical periodontitis. The endodontic pathogens Porphyromonas endodontalis, Fusobacterium nucleatum and Treponema denticola were quantified by real time polymerase chain reaction (qPCR). The prevalence of each species was identified at both a low detection threshold (>50 bacteria) and a high detection threshold (>1000 bacteria). Results: 75 patients (mean age 30.1 yrs SD 10.1) were included in the analysis. The most prevalent bacterium at both the low and high threshold was F. nucleatum followed by T. denticola at the low threshold and P. endodontalis at the high threshold. There was no association with symptoms at the low detection threshold, but at high threshold P. endodontalis was associated with swelling, adjusted odds ratio (OR), 9.32 95%CI 1.11- 78.66, P=0.04. All species were more prevalent in apical periodontitis due to caries only at the low detection threshold, OR=5.01 (P=0.006) for T. denticola; 4.84 (P=0.01) for F. nucleatum; and 3.62 (P=0.03) for P. endodontalis. Conclusion: There was a high prevalence of the F. nucleatum, T. denticola and P. endodontalis in apical periodontitis associated with caries. None of these bacterial were associated with pain but the presence of P. endodontalis at high levels was associated with swelling.

Research paper thumbnail of Identification of Risk Factors Associated with Resistant Escherichia coli Isolates from Poultry Farms in the East Coast of Peninsular Malaysia: A Cross Sectional Study

Antibiotics

Antimicrobial resistance is of concern to global health security worldwide. We aimed to identify ... more Antimicrobial resistance is of concern to global health security worldwide. We aimed to identify the prevalence, resistance patterns, and risk factors associated with Escherichia coli (E. coli) resistance from poultry farms in Kelantan, Terengganu, and Pahang states of east coast peninsular Malaysia. Between 8 February 2019 and 23 February 2020, a total of 371 samples (cloacal swabs = 259; faecal = 84; Sewage = 14, Tap water = 14) were collected. Characteristics of the sampled farms including management type, biosecurity, and history of disease were obtained using semi-structured questionnaire. Presumptive E. coli isolates were identified based on colony morphology with subsequent biochemical and PCR confirmation. Susceptibility of isolates was tested against a panel of 12 antimicrobials and interpreted alongside risk factor data obtained from the surveys. We isolated 717 E. coli samples from poultry and environmental samples. Our findings revealed that cloacal (17.8%, 46/259), faec...

Research paper thumbnail of Antimicrobial resistance preparedness in sub-Saharan African countries

Antimicrobial Resistance & Infection Control

Background Antimicrobial resistance (AMR) is of growing concern globally and AMR status in sub-Sa... more Background Antimicrobial resistance (AMR) is of growing concern globally and AMR status in sub-Saharan Africa (SSA) is undefined due to a lack of real-time data recording, surveillance and regulation. World Health Organization (WHO) Joint External Evaluation (JEE) reports are voluntary, collaborative processes to assess country capacities and preparedness to prevent, detect and rapidly respond to public health risks, including AMR. The data from SSA JEE reports were analysed to gain an overview of how SSA is working towards AMR preparedness and where strengths and weaknesses lie. Methods SSA country JEE AMR preparedness scores were analysed. A cumulative mean of all the SSA country AMR preparedness scores was calculated and compared to the overall mean SSA JEE score. AMR preparedness indicators were analysed, and data were weighted by region. Findings The mean SSA AMR preparedness score was 53% less than the overall mean SSA JEE score. East Africa had the highest percentage of count...

Research paper thumbnail of Lockdown measures in response to COVID-19 in Sub-Saharan Africa: A rapid study of nine countries

Lockdown measures have been introduced worldwide to contain the transmission of COVID-19. This pa... more Lockdown measures have been introduced worldwide to contain the transmission of COVID-19. This paper defines the term lockdown and describes the design, timing and implementation of lockdown in nine countries in Sub Saharan Africa: Ghana, Nigeria, South Africa, Sierra Leone, Sudan, Tanzania, Uganda, Zambia and Zimbabwe. It also discusses the manner in which lockdown is enforced, the need to mitigate the harms of lockdown, and the association between lockdown and the reported number of COVID-19 cases and deaths. While there are some commonalities in the implementation of lockdown, a more notable finding is the variation in the design, timing and implementation of lockdown measures across the nine countries. We found that the number of reported cases is heavily dependent on the number of tests done, and that testing rates ranged from 9 to 21,261 per million population. The reported number of COVID-19 deaths per million population also varies, but is generally low when compared to coun...

Research paper thumbnail of Extensive genetic diversity in Plasmodium vivax from Sudan and its genetic relationships with other geographical isolates

Plasmodium vivax malaria is a neglected tropical disease in Africa due to low occurrence rates an... more Plasmodium vivax malaria is a neglected tropical disease in Africa due to low occurrence rates and lack of accurate diagnosis. Recently, there has been a dramatic increase in P. vivax cases in East Africa and reportedly spreading to western countries. This study investigated the geographical origin and genetic diversity of P. vivax in Sudan by 14 microsatellite markers. A total of 113 clinical P. vivax samples were collected from two districts, New Halfa and Khartoum in Sudan. In addition, data from 841 geographical samples retrieved from the database for global genetic analysis were included in the analysis to further the genetic relationships among the P. vivax isolates at regional and worldwide scales. On a regional scale, we observed 91 unique and 8 shared haplotypes amongst the Sudan samples. Such a high genetic diversity compared to other geographical isolates lends support to hypothesis that P. vivax was originated from Africa. On a global scale, as already demonstrated, we o...

Research paper thumbnail of Is Africa prepared for tackling the COVID-19 (SARS-CoV-2) epidemic. Lessons from past outbreaks, ongoing pan-African public health efforts, and implications for the future

International Journal of Infectious Diseases

Research paper thumbnail of Human Plasmodium vivax diversity, population structure and evolutionary origin

PLOS Neglected Tropical Diseases

More than 200 million malaria clinical cases are reported each year due to Plasmodium vivax, the ... more More than 200 million malaria clinical cases are reported each year due to Plasmodium vivax, the most widespread Plasmodium species in the world. This species has been neglected and understudied for a long time, due to its lower mortality in comparison with Plasmodium falciparum. A renewed interest has emerged in the past decade with the discovery of antimalarial drug resistance and of severe and even fatal human cases. Nonetheless, today there are still significant gaps in our understanding of the population genetics and evolutionary history of P. vivax, particularly because of a lack of genetic data from PLOS NEGLECTED TROPICAL DISEASES

Research paper thumbnail of Assessment of Plasmodium falciparum drug resistance molecular markers from the Blue Nile State, Southeast Sudan

Malaria Journal

Background Plasmodium falciparum malaria is a public health problem worldwide. Malaria treatment ... more Background Plasmodium falciparum malaria is a public health problem worldwide. Malaria treatment policy has faced periodic changes due to emergence of drug resistant parasites. In Sudan chloroquine has been replaced by artesunate and sulfadoxine/pyrimethamine (AS/SP) in 2005 and to artemether–lumefantrine (AL) in 2017, due to the development of drug resistance. Different molecular markers have been used to monitor the status of drug resistant P. falciparum. This study aimed to determine the frequency of malaria drug resistance molecular markers in Southeast Sudan. Methods The samples of this study were day zero dried blood spot samples collected from efficacy studies in the Blue Nile State from November 2015 to January 2016. A total of 130 samples were amplified and sequenced using illumina Miseq platform. The molecular markers included were Pfcrt, Pfmdr1, Pfdhfr, Pfdhps, Pfk13, exonuclease and artemisinin resistant (ART‐R) genetic background (Pfmdr2, ferroredoxine, Pfcrt and Pfarps...

Research paper thumbnail of Prevalence of 3.7 and 4.2 Deletions in Sudanese Patients with Red Cells Hypochromia and Microcytosis

Objective: Alpha-thalassemia is a genetic disorder characterized by deletions of one or more α gl... more Objective: Alpha-thalassemia is a genetic disorder characterized by deletions of one or more α globin genes that result in deficient of α globin chains reducing haemoglobin concentration. The study aimed to screen 97 patients with microcytosis and hypochromasia for the 3.7 and 4.2 alpha thalassemia deletion mutations. Results: Out of 97 patients screened, only 7 were carriers for the 3.7 deletion and all patients were negative for the 4.2 deletion. The 3.7 deletion was found in Foor, Hawsa and Rezagat Sudanese tribes. In the carriers of the 3.7 deletion, Red Blood Cells and Haematocrit were significantly increased. The Red Blood Cells were 7.23±0.78×10 12 /L in adult males and 7.21±0.67×10 12 /L in adult females while in children were 5.07±0.87×10 12 /L. The mean cell volume and mean cell haemoglobin were significantly decreased, but the mean cell haemoglobin concentration slightly decreased. Haemoglobin levels didn’t revealed statistically significant decrease in adult males (11.7±...

Research paper thumbnail of Genetic Diversity of the cagA gene of Helicobacter pylori strains from Sudanese Patients with Different Gastroduodenal Diseases

Background: There is an increase in the prevalence of Helicobacter pylori infection in Sudan, acc... more Background: There is an increase in the prevalence of Helicobacter pylori infection in Sudan, accompanied by a high incidence of upper gastrointestinal malignancy. The cytotoxin-associated gene cagA gene is a marker of a pathogenicity island (PAI) in H. pylori and plays a crucial role in determining the clinical outcome of Helicobacter infections. Objective: This study aimed to determine the frequency and heterogeneity of the cagA gene of H. pylori and correlate the presence of cagA gene with clinical outcomes. Materials and methods: Fifty endoscopy biopsies were collected from Fedail and Soba hospitals in Khartoum state. DNA was extracted using the Guanidine chloride method followed by PCR to amplify 16S rRNA and cagA gene of H. pylori using specific primers. DNA amplicons of cagA gene were purified and sequenced. Bioinformatics and statistical analysis were done to characterize and to test the association between cagA gene and gastric complications. Results: CagA gene was detected...

Research paper thumbnail of Identifying asymptomatic Leishmania infections in non-endemic villages in Gedaref state, Sudan

BMC Research Notes

Objectives Infection with the causative agent of visceral leishmaniasis (VL) may be either sympto... more Objectives Infection with the causative agent of visceral leishmaniasis (VL) may be either symptomatic or asymptomatic. In this study we aimed at investigating the prevalence of asymptomatic infections of leishmania in non-endemic villages in Gedaref state, Sudan. A descriptive cross-sectional study conducted during September and October 2014. Blood samples were collected for serological and molecular analysis. Sticky-traps, knockdown spray and CDC-miniature light traps were used for the collection of sandflies. Results Ninety-Five participants were included; 52 from Abukishma, 15 Algadamblia Tirfa, 25 Abualnaja and 3 were from Algadamblia Aljabal. Females constituted 56 (58.9%) of the study participants while males were 39 (41.1%). The most frequent age group was > 40-years (54.7%). Balanites/Acacia trees were the most planted tree inside the houses; 78 (82.1%). Also, 85 (89.5%) of the participants breed animals inside the house. DAT test revealed 5 positive participants (5.2%)....

Research paper thumbnail of Malaria and Burkitt’s Lymphoma: An In Silico Analysis of Gene Expression Links between Malaria and Burkitt’s Lymphoma and Potential Anticancer Activity of Artemisinin Derivatives

BackgroundBurkitt’s lymphoma (BL) is an aggressive form of B-cell non-Hodgkin lymphoma. Endemic s... more BackgroundBurkitt’s lymphoma (BL) is an aggressive form of B-cell non-Hodgkin lymphoma. Endemic subtype of the disease showed a remarkable statistical and epidemiological association with malaria infection. Despite the numerous studies performed to explain this association; molecular mechanisms underlie such coincidence still remain unclear. Dissecting molecular mechanisms which link Malaria infection and Burkitt’s lymphoma can provide insights about reported anticancer action of certain antimalarial drugs, namely artemisinin derivatives.MethodsHere we applied an integrative approach to investigate for potential links between malaria infection and endemic Burkitt’s lymphoma regarding their gene expression, and further explore common molecular mechanisms through which artemisinin compounds might act in endemic Burkitt’s lymphoma. Using gene expression data of malaria (Plasmodium falciparum infected erythroblasts) and endemic Burkitt’s lymphoma from Gene Expression Omnibus database, e...

Research paper thumbnail of Distribution of Duffy Phenotypes among Plasmodium vivax Infections in Sudan

Genes

Negative Duffy expression on the surface of human red blood cells was believed to be a barrier fo... more Negative Duffy expression on the surface of human red blood cells was believed to be a barrier for Plasmodium vivax infection in most Africans. However, P. vivax has been demonstrated to infect Duffy-negative individuals in several Central and East African countries. In this study, we investigated the distribution of Duffy blood group phenotypes with regard to P. vivax infection and parasitemia in Sudan. Out of 992 microscopic-positive malaria samples, 190 were identified as P. vivax positive infections. Among them, 186 were P. vivax mono-infections and 4 were mixed P. vivax and Plasmodium falciparum infections. A subset of 77 samples was estimated with parasitemia by quantitative real-time PCR. Duffy codons were sequenced from the 190 P. vivax positive samples. We found that the Duffy Fy(a-b+) phenotype was the most prevalent, accounting for 67.9% of all P. vivax infections, while homozygous Duffy-negative Fy(a-b-) accounted for 17.9% of the P. vivax infections. The prevalence of i...

Research paper thumbnail of ’ s response to reviews Title : Monoallelic Characteristic-Bearing Heterozygous L 1053 X in BRCA 2 Gene among Sudanese women with Breast Cancer

Research paper thumbnail of Prevalence of glucose-6-phosphate dehydrogenase deficiency (G6PDd), CareStart qualitative rapid diagnostic test performance, and genetic variants in two malaria-endemic areas in Sudan

PLOS Neglected Tropical Diseases

Glucose-6-phosphate dehydrogenase deficiency (G6PDd) is the most common enzymopathy globally, and... more Glucose-6-phosphate dehydrogenase deficiency (G6PDd) is the most common enzymopathy globally, and deficient individuals may experience severe hemolysis following treatment with 8-aminoquinolines. With increasing evidence of Plasmodium vivax infections throughout sub-Saharan Africa, there is a pressing need for population-level data at on the prevalence of G6PDd. Such evidence-based data will guide the expansion of primaquine and potentially tafenoquine for radical cure of P. vivax infections. This study aimed to quantify G6PDd prevalence in two geographically distinct areas in Sudan, and evaluating the performance of a qualitative CareStart rapid diagnostic test as a point-of-care test. Blood samples were analyzed from 491 unrelated healthy persons in two malaria-endemic sites in eastern and central Sudan. A pre-structured questionnaire was used which included demographic data, risk factors and treatment history. G6PD levels were measured using spectrophotometry (SPINREACT) and firs...

Research paper thumbnail of Abstracts of the Eighth EDCTP Forum, 6–9 November 2016

S OF PLENARY PRESENTATIONS A3 ABSTRACTS OF ORAL PRESENTATIONS A5S OF ORAL PRESENTATIONS A5 ABSTRA... more S OF PLENARY PRESENTATIONS A3 ABSTRACTS OF ORAL PRESENTATIONS A5S OF ORAL PRESENTATIONS A5 ABSTRACTS OF POSTER PRESENTATIONS A16S OF POSTER PRESENTATIONS A16

Research paper thumbnail of Invasive Malaria Vector Anopheles stephensi Mosquitoes in Sudan, 2016–2018

Emerging Infectious Diseases

Anopheles stephensi mosquitoes are urban malaria vectors in Asia that have recently invaded the H... more Anopheles stephensi mosquitoes are urban malaria vectors in Asia that have recently invaded the Horn of Africa. We detected emergence of An. stephensi mosquitoes in 2 noncontiguous states of eastern Sudan. Results of mitochondrial DNA sequencing suggest the possibility of distinct invasions, potentially from a neighboring country.

Research paper thumbnail of Socio-Ecological Systems Analysis and Health System Readiness in Responding to Dengue Epidemics in Ilala and Kinondoni Districts, Tanzania

Frontiers in Tropical Diseases

IntroductionSince 2010, Tanzania has been experiencing frequent outbreaks of dengue. The objectiv... more IntroductionSince 2010, Tanzania has been experiencing frequent outbreaks of dengue. The objectives of this study were to carry out a socio-ecological systems (SES) analysis to identify risk factors and interventions and assess the readiness of the district in the prevention and control of dengue.MethodsThe study utilized a cross-sectional purposive selection of key stakeholders responsible for disease surveillance and response in human and animal sectors in Ilala and Kinondoni districts in Tanzania. A SES framework was used to identify drivers and construct perceived thematic causal explanations of the dengue outbreaks in the study districts. A mapping exercise was carried out to analyse the performance of the disease surveillance system at district and facility levels. A semi-structured questionnaire was used to assess the districts’ readiness in the response to dengue outbreak.ResultsThe two districts were characterized by both urban and peri-urban ecosystems, with a mixture of p...

Research paper thumbnail of Socio-ecological Systems Analysis of the Prevention and Control of Dengue in two Districts of Dar es Salaam City, Tanzania

Background: Since 2010, Tanzania has been experiencing frequent outbreaks of dengue. The objectiv... more Background: Since 2010, Tanzania has been experiencing frequent outbreaks of dengue. The objective of this study was to carry out a socio-ecological systems analysis and assess the readiness in dengue prevention and control in Kinondoni and Ilala districts of Dar es Salaam City, Tanzania.Methods: Twenty-seven key district officials responsible for human and animal health were involved in a socio-ecological systems framework analysis as regards to dengue. In addition, the readiness of the districts to respond to dengue outbreaks and the performance of the disease surveillance system was assessed.Results: The two districts were characterized by both urban and peri-urban ecosystems, with a mixture of planned and unplanned settlements which support breeding and proliferation of Aedes mosquitoes. The results indicate inadequate levels of readiness in the management and control of dengue outbreaks, in terms of clinical competence, diagnostic capacities, surveillance system and control/pre...

Research paper thumbnail of Detection and characterization of carbapenem resistant Gram‐negative bacilli isolates recovered from hospitalized patients at Soba University Hospital, Sudan

BMC Microbiology

Background Antimicrobial resistance (AMR) poses a complex threat to global health security and un... more Background Antimicrobial resistance (AMR) poses a complex threat to global health security and universal health coverage. Recently, nosocomial infections with carbapenemase-producing Gram-negative bacilli (GNB) is increasing worldwide. We report the molecular characterization and detection of genes associated with carbapenemase producing Gram negative bacteria isolated from hospitalized patients at Soba University Hospital (SUH) in Khartoum State, Sudan. Results Between October 2016 and February 2017, a total of 206 GNB clinical specimens were collected from hospitalized patients in SUH. Of 206 carbapenem resistance isolates, 171 (83 %) were confirmed as phenotypically resistant and 121 (58.7 %) isolates harboured one or more carbapenemase genes. New Delhi metallo-β-lactamase (NDM) types were the most predominant genes, blaNDM 107(52 %), followed by blaIMP 7 (3.4 %), blaOXA-48 5(2.4 %) and blaVIM 2 (0.9 %). Co-resistance genes with NDM producing GNB were detected in 87 (81.3 %) of a...

Research paper thumbnail of Quantitative analysis of candidate endodontic pathogens and their association with cause and symptoms of apical periodontitis in a Sudanese population

European Endodontic Journal

Objective: To investigate the prevalence of key endodontic pathogens and their association with t... more Objective: To investigate the prevalence of key endodontic pathogens and their association with the clinical features and the cause of apical periodontitis. Methods: The study population included patients referred to Khartoum Dental teaching Hospital, Sudan for endodontic treatment. Samples were collected from single-rooted teeth carious or traumatised teeth with clinical and radiographic evidence of apical periodontitis. The endodontic pathogens Porphyromonas endodontalis, Fusobacterium nucleatum and Treponema denticola were quantified by real time polymerase chain reaction (qPCR). The prevalence of each species was identified at both a low detection threshold (>50 bacteria) and a high detection threshold (>1000 bacteria). Results: 75 patients (mean age 30.1 yrs SD 10.1) were included in the analysis. The most prevalent bacterium at both the low and high threshold was F. nucleatum followed by T. denticola at the low threshold and P. endodontalis at the high threshold. There was no association with symptoms at the low detection threshold, but at high threshold P. endodontalis was associated with swelling, adjusted odds ratio (OR), 9.32 95%CI 1.11- 78.66, P=0.04. All species were more prevalent in apical periodontitis due to caries only at the low detection threshold, OR=5.01 (P=0.006) for T. denticola; 4.84 (P=0.01) for F. nucleatum; and 3.62 (P=0.03) for P. endodontalis. Conclusion: There was a high prevalence of the F. nucleatum, T. denticola and P. endodontalis in apical periodontitis associated with caries. None of these bacterial were associated with pain but the presence of P. endodontalis at high levels was associated with swelling.

Research paper thumbnail of Identification of Risk Factors Associated with Resistant Escherichia coli Isolates from Poultry Farms in the East Coast of Peninsular Malaysia: A Cross Sectional Study

Antibiotics

Antimicrobial resistance is of concern to global health security worldwide. We aimed to identify ... more Antimicrobial resistance is of concern to global health security worldwide. We aimed to identify the prevalence, resistance patterns, and risk factors associated with Escherichia coli (E. coli) resistance from poultry farms in Kelantan, Terengganu, and Pahang states of east coast peninsular Malaysia. Between 8 February 2019 and 23 February 2020, a total of 371 samples (cloacal swabs = 259; faecal = 84; Sewage = 14, Tap water = 14) were collected. Characteristics of the sampled farms including management type, biosecurity, and history of disease were obtained using semi-structured questionnaire. Presumptive E. coli isolates were identified based on colony morphology with subsequent biochemical and PCR confirmation. Susceptibility of isolates was tested against a panel of 12 antimicrobials and interpreted alongside risk factor data obtained from the surveys. We isolated 717 E. coli samples from poultry and environmental samples. Our findings revealed that cloacal (17.8%, 46/259), faec...

Research paper thumbnail of Antimicrobial resistance preparedness in sub-Saharan African countries

Antimicrobial Resistance & Infection Control

Background Antimicrobial resistance (AMR) is of growing concern globally and AMR status in sub-Sa... more Background Antimicrobial resistance (AMR) is of growing concern globally and AMR status in sub-Saharan Africa (SSA) is undefined due to a lack of real-time data recording, surveillance and regulation. World Health Organization (WHO) Joint External Evaluation (JEE) reports are voluntary, collaborative processes to assess country capacities and preparedness to prevent, detect and rapidly respond to public health risks, including AMR. The data from SSA JEE reports were analysed to gain an overview of how SSA is working towards AMR preparedness and where strengths and weaknesses lie. Methods SSA country JEE AMR preparedness scores were analysed. A cumulative mean of all the SSA country AMR preparedness scores was calculated and compared to the overall mean SSA JEE score. AMR preparedness indicators were analysed, and data were weighted by region. Findings The mean SSA AMR preparedness score was 53% less than the overall mean SSA JEE score. East Africa had the highest percentage of count...

Research paper thumbnail of Lockdown measures in response to COVID-19 in Sub-Saharan Africa: A rapid study of nine countries

Lockdown measures have been introduced worldwide to contain the transmission of COVID-19. This pa... more Lockdown measures have been introduced worldwide to contain the transmission of COVID-19. This paper defines the term lockdown and describes the design, timing and implementation of lockdown in nine countries in Sub Saharan Africa: Ghana, Nigeria, South Africa, Sierra Leone, Sudan, Tanzania, Uganda, Zambia and Zimbabwe. It also discusses the manner in which lockdown is enforced, the need to mitigate the harms of lockdown, and the association between lockdown and the reported number of COVID-19 cases and deaths. While there are some commonalities in the implementation of lockdown, a more notable finding is the variation in the design, timing and implementation of lockdown measures across the nine countries. We found that the number of reported cases is heavily dependent on the number of tests done, and that testing rates ranged from 9 to 21,261 per million population. The reported number of COVID-19 deaths per million population also varies, but is generally low when compared to coun...

Research paper thumbnail of Extensive genetic diversity in Plasmodium vivax from Sudan and its genetic relationships with other geographical isolates

Plasmodium vivax malaria is a neglected tropical disease in Africa due to low occurrence rates an... more Plasmodium vivax malaria is a neglected tropical disease in Africa due to low occurrence rates and lack of accurate diagnosis. Recently, there has been a dramatic increase in P. vivax cases in East Africa and reportedly spreading to western countries. This study investigated the geographical origin and genetic diversity of P. vivax in Sudan by 14 microsatellite markers. A total of 113 clinical P. vivax samples were collected from two districts, New Halfa and Khartoum in Sudan. In addition, data from 841 geographical samples retrieved from the database for global genetic analysis were included in the analysis to further the genetic relationships among the P. vivax isolates at regional and worldwide scales. On a regional scale, we observed 91 unique and 8 shared haplotypes amongst the Sudan samples. Such a high genetic diversity compared to other geographical isolates lends support to hypothesis that P. vivax was originated from Africa. On a global scale, as already demonstrated, we o...

Research paper thumbnail of Is Africa prepared for tackling the COVID-19 (SARS-CoV-2) epidemic. Lessons from past outbreaks, ongoing pan-African public health efforts, and implications for the future

International Journal of Infectious Diseases

Research paper thumbnail of Human Plasmodium vivax diversity, population structure and evolutionary origin

PLOS Neglected Tropical Diseases

More than 200 million malaria clinical cases are reported each year due to Plasmodium vivax, the ... more More than 200 million malaria clinical cases are reported each year due to Plasmodium vivax, the most widespread Plasmodium species in the world. This species has been neglected and understudied for a long time, due to its lower mortality in comparison with Plasmodium falciparum. A renewed interest has emerged in the past decade with the discovery of antimalarial drug resistance and of severe and even fatal human cases. Nonetheless, today there are still significant gaps in our understanding of the population genetics and evolutionary history of P. vivax, particularly because of a lack of genetic data from PLOS NEGLECTED TROPICAL DISEASES

Research paper thumbnail of Assessment of Plasmodium falciparum drug resistance molecular markers from the Blue Nile State, Southeast Sudan

Malaria Journal

Background Plasmodium falciparum malaria is a public health problem worldwide. Malaria treatment ... more Background Plasmodium falciparum malaria is a public health problem worldwide. Malaria treatment policy has faced periodic changes due to emergence of drug resistant parasites. In Sudan chloroquine has been replaced by artesunate and sulfadoxine/pyrimethamine (AS/SP) in 2005 and to artemether–lumefantrine (AL) in 2017, due to the development of drug resistance. Different molecular markers have been used to monitor the status of drug resistant P. falciparum. This study aimed to determine the frequency of malaria drug resistance molecular markers in Southeast Sudan. Methods The samples of this study were day zero dried blood spot samples collected from efficacy studies in the Blue Nile State from November 2015 to January 2016. A total of 130 samples were amplified and sequenced using illumina Miseq platform. The molecular markers included were Pfcrt, Pfmdr1, Pfdhfr, Pfdhps, Pfk13, exonuclease and artemisinin resistant (ART‐R) genetic background (Pfmdr2, ferroredoxine, Pfcrt and Pfarps...

Research paper thumbnail of Prevalence of 3.7 and 4.2 Deletions in Sudanese Patients with Red Cells Hypochromia and Microcytosis

Objective: Alpha-thalassemia is a genetic disorder characterized by deletions of one or more α gl... more Objective: Alpha-thalassemia is a genetic disorder characterized by deletions of one or more α globin genes that result in deficient of α globin chains reducing haemoglobin concentration. The study aimed to screen 97 patients with microcytosis and hypochromasia for the 3.7 and 4.2 alpha thalassemia deletion mutations. Results: Out of 97 patients screened, only 7 were carriers for the 3.7 deletion and all patients were negative for the 4.2 deletion. The 3.7 deletion was found in Foor, Hawsa and Rezagat Sudanese tribes. In the carriers of the 3.7 deletion, Red Blood Cells and Haematocrit were significantly increased. The Red Blood Cells were 7.23±0.78×10 12 /L in adult males and 7.21±0.67×10 12 /L in adult females while in children were 5.07±0.87×10 12 /L. The mean cell volume and mean cell haemoglobin were significantly decreased, but the mean cell haemoglobin concentration slightly decreased. Haemoglobin levels didn’t revealed statistically significant decrease in adult males (11.7±...

Research paper thumbnail of Genetic Diversity of the cagA gene of Helicobacter pylori strains from Sudanese Patients with Different Gastroduodenal Diseases

Background: There is an increase in the prevalence of Helicobacter pylori infection in Sudan, acc... more Background: There is an increase in the prevalence of Helicobacter pylori infection in Sudan, accompanied by a high incidence of upper gastrointestinal malignancy. The cytotoxin-associated gene cagA gene is a marker of a pathogenicity island (PAI) in H. pylori and plays a crucial role in determining the clinical outcome of Helicobacter infections. Objective: This study aimed to determine the frequency and heterogeneity of the cagA gene of H. pylori and correlate the presence of cagA gene with clinical outcomes. Materials and methods: Fifty endoscopy biopsies were collected from Fedail and Soba hospitals in Khartoum state. DNA was extracted using the Guanidine chloride method followed by PCR to amplify 16S rRNA and cagA gene of H. pylori using specific primers. DNA amplicons of cagA gene were purified and sequenced. Bioinformatics and statistical analysis were done to characterize and to test the association between cagA gene and gastric complications. Results: CagA gene was detected...

Research paper thumbnail of Identifying asymptomatic Leishmania infections in non-endemic villages in Gedaref state, Sudan

BMC Research Notes

Objectives Infection with the causative agent of visceral leishmaniasis (VL) may be either sympto... more Objectives Infection with the causative agent of visceral leishmaniasis (VL) may be either symptomatic or asymptomatic. In this study we aimed at investigating the prevalence of asymptomatic infections of leishmania in non-endemic villages in Gedaref state, Sudan. A descriptive cross-sectional study conducted during September and October 2014. Blood samples were collected for serological and molecular analysis. Sticky-traps, knockdown spray and CDC-miniature light traps were used for the collection of sandflies. Results Ninety-Five participants were included; 52 from Abukishma, 15 Algadamblia Tirfa, 25 Abualnaja and 3 were from Algadamblia Aljabal. Females constituted 56 (58.9%) of the study participants while males were 39 (41.1%). The most frequent age group was > 40-years (54.7%). Balanites/Acacia trees were the most planted tree inside the houses; 78 (82.1%). Also, 85 (89.5%) of the participants breed animals inside the house. DAT test revealed 5 positive participants (5.2%)....

Research paper thumbnail of Malaria and Burkitt’s Lymphoma: An In Silico Analysis of Gene Expression Links between Malaria and Burkitt’s Lymphoma and Potential Anticancer Activity of Artemisinin Derivatives

BackgroundBurkitt’s lymphoma (BL) is an aggressive form of B-cell non-Hodgkin lymphoma. Endemic s... more BackgroundBurkitt’s lymphoma (BL) is an aggressive form of B-cell non-Hodgkin lymphoma. Endemic subtype of the disease showed a remarkable statistical and epidemiological association with malaria infection. Despite the numerous studies performed to explain this association; molecular mechanisms underlie such coincidence still remain unclear. Dissecting molecular mechanisms which link Malaria infection and Burkitt’s lymphoma can provide insights about reported anticancer action of certain antimalarial drugs, namely artemisinin derivatives.MethodsHere we applied an integrative approach to investigate for potential links between malaria infection and endemic Burkitt’s lymphoma regarding their gene expression, and further explore common molecular mechanisms through which artemisinin compounds might act in endemic Burkitt’s lymphoma. Using gene expression data of malaria (Plasmodium falciparum infected erythroblasts) and endemic Burkitt’s lymphoma from Gene Expression Omnibus database, e...

Research paper thumbnail of Distribution of Duffy Phenotypes among Plasmodium vivax Infections in Sudan

Genes

Negative Duffy expression on the surface of human red blood cells was believed to be a barrier fo... more Negative Duffy expression on the surface of human red blood cells was believed to be a barrier for Plasmodium vivax infection in most Africans. However, P. vivax has been demonstrated to infect Duffy-negative individuals in several Central and East African countries. In this study, we investigated the distribution of Duffy blood group phenotypes with regard to P. vivax infection and parasitemia in Sudan. Out of 992 microscopic-positive malaria samples, 190 were identified as P. vivax positive infections. Among them, 186 were P. vivax mono-infections and 4 were mixed P. vivax and Plasmodium falciparum infections. A subset of 77 samples was estimated with parasitemia by quantitative real-time PCR. Duffy codons were sequenced from the 190 P. vivax positive samples. We found that the Duffy Fy(a-b+) phenotype was the most prevalent, accounting for 67.9% of all P. vivax infections, while homozygous Duffy-negative Fy(a-b-) accounted for 17.9% of the P. vivax infections. The prevalence of i...