16 results on '"Jarra Manneh"'
Search Results
2. Transcriptome analysis reveals molecular targets of erythrocyte invasion phenotype diversity in natural Plasmodium falciparum isolates from Cameroon
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Ines A. Ngoh, Karim Mane, Jarra Manneh, Fatoumata Bojang, Aminata S. Jawara, Theresia N. Akenji, Damian N. Anong, Umberto D’Alessandro, and Alfred Amambua-Ngwa
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Plasmodium falciparum ,transcriptome ,RBC invasion ,phenotype diversity ,malaria ,vaccine targets ,Infectious and parasitic diseases ,RC109-216 - Abstract
Further understanding of the molecular mediators of alternative RBC invasion phenotypes in endemic malaria parasites will support malaria blood-stage vaccine or drug development. This study investigated the prevalence of sialic acid (SA)-dependent and SA-independent RBC invasion pathways in endemic Plasmodium falciparum parasites from Cameroon and compared the schizont stage transcriptomes in these two groups to uncover the wider repertoire of transcriptional variation associated with the use of alternative RBC invasion pathway phenotypes. A two-color flow cytometry-based invasion-inhibition assay against RBCs treated with neuraminidase, trypsin, and chymotrypsin and deep RNA sequencing of schizont stages harvested in the first ex vivo replication cycle in culture were employed in this investigation. RBC invasion phenotypes were determined for 63 isolates from asymptomatic children with uncomplicated malaria. Approximately 80% of the isolates invaded neuraminidase-treated but not chymotrypsin-treated RBCs, representing SA-independent pathways of RBC invasion. The schizont transcriptome profiles of 16 isolates with invasion phenotypes revealed a total of 5,136 gene transcripts, with 85% of isolates predicted at schizont stages. Two distinct transcriptome profile clusters belonging to SA-dependent and SA-independent parasites were obtained by data reduction with principal component analysis. Differential analysis of gene expression between the two clusters implicated, in addition to the well-characterized adhesins, the upregulation of genes encoding proteins mediating merozoite organelle discharges as well as several conserved, virulent, merozoite-associated, and exported proteins. The latter majority have been shown to have structural and physiological relevance to RBC surface remodeling and immune evasion in malaria and thus have potential as anti-invasion targets.
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- 2024
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3. Genomic epidemiology of SARS-CoV-2 infections in The Gambia: an analysis of routinely collected surveillance data between March, 2020, and January, 2022
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Abdoulie Kanteh, MSc, Haruna S Jallow, MSc, Jarra Manneh, MSc, Bakary Sanyang, BSc, Mariama A Kujabi, MSc, Sainabou Laye Ndure, BSc, Sheikh Jarju, DVM, Alhagie Papa Sey, HND, Dabiri Damilare K, BSc, Yaya Bah, BSc, Sana Sambou, MSc, Gibril Jarju, MSc, Buba Manjang, PhD, Abubacarr Jagne, MD, Sheikh Omar Bittaye, MD, Mustapha Bittaye, FWACS, Karen Forrest, MD, Desta Alamerew Tiruneh, MPH, Ahmadou Lamin Samateh, MD, Sheriffo Jagne, PhD, Stéphane Hué, PhD, Nuredin Mohammed, PhD, Alfred Amambua-Ngwa, PhD, Beate Kampmann, ProfPhD, Umberto D'Alessandro, ProfPhD, Thushan I de Silva, PhD, Anna Roca, ProfPhD, and Abdul Karim Sesay, PhD
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Public aspects of medicine ,RA1-1270 - Abstract
Summary: Background: COVID-19, caused by SARS-CoV-2, is one of the deadliest pandemics of the past 100 years. Genomic sequencing has an important role in monitoring of the evolution of the virus, including the detection of new viral variants. We aimed to describe the genomic epidemiology of SARS-CoV-2 infections in The Gambia. Methods: Nasopharyngeal or oropharyngeal swabs collected from people with suspected cases of COVID-19 and international travellers were tested for SARS-CoV-2 with standard RT-PCR methods. SARS-CoV-2-positive samples were sequenced according to standard library preparation and sequencing protocols. Bioinformatic analysis was done using ARTIC pipelines and Pangolin was used to assign lineages. To construct phylogenetic trees, sequences were first stratified into different COVID-19 waves (waves 1–4) and aligned. Clustering analysis was done and phylogenetic trees constructed. Findings: Between March, 2020, and January, 2022, 11 911 confirmed cases of COVID-19 were recorded in The Gambia, and 1638 SARS-CoV-2 genomes were sequenced. Cases were broadly distributed into four waves, with more cases during the waves that coincided with the rainy season (July–October). Each wave occurred after the introduction of new viral variants or lineages, or both, generally those already established in Europe or in other African countries. Local transmission was higher during the first and third waves (ie, those that corresponded with the rainy season), in which the B.1.416 lineage and delta (AY.34.1) were dominant, respectively. The second wave was driven by the alpha and eta variants and the B.1.1.420 lineage. The fourth wave was driven by the omicron variant and was predominantly associated with the BA.1.1 lineage. Interpretation: More cases of SARS-CoV-2 infection were recorded in The Gambia during peaks of the pandemic that coincided with the rainy season, in line with transmission patterns for other respiratory viruses. The introduction of new lineages or variants preceded epidemic waves, highlighting the importance of implementing well structured genomic surveillance at a national level to detect and monitor emerging and circulating variants. Funding: Medical Research Unit The Gambia at London School of Hygiene & Tropical Medicine, UK Research and Innovation, WHO.
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- 2023
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4. Genomic Characterization of Skin and Soft Tissue Streptococcus pyogenes Isolates from a Low-Income and a High-Income Setting
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Saikou Y. Bah, Alexander J. Keeley, Edwin P. Armitage, Henna Khalid, Roy R. Chaudhuri, Elina Senghore, Jarra Manneh, Lisa Tilley, Michael Marks, Saffiatou Darboe, Abdul K. Sesay, Thushan I. de Silva, and Claire E. Turner
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FCT region ,bacterial genomics ,emm types ,group A Streptococcus ,skin infection ,vaccine ,Microbiology ,QR1-502 - Abstract
ABSTRACT Streptococcus pyogenes is a leading cause of human morbidity and mortality, especially in resource-limited settings. The development of a vaccine against S. pyogenes is a global health priority to reduce the burden of postinfection rheumatic heart disease. To support this, molecular characterization of circulating S. pyogenes isolates is needed. We performed whole-genome analyses of S. pyogenes isolates from skin and soft tissue infections in Sukuta, The Gambia, a low-income country (LIC) in West Africa where there is a high burden of such infections. To act as a comparator to these LIC isolates, skin infection isolates from Sheffield, United Kingdom (a high-income country [HIC]), were also sequenced. The LIC isolates from The Gambia were genetically more diverse (46 emm types in 107 isolates) than the HIC isolates from Sheffield (23 emm types in 142 isolates), with only 7 overlapping emm types. Other molecular markers were shared, including a high prevalence of the skin infection-associated emm pattern D and the variable fibronectin-collagen-T antigen (FCT) types FCT-3 and FCT-4. Fewer of the Gambian LIC isolates carried prophage-associated superantigens (64%) and DNases (26%) than did the Sheffield HIC isolates (99% and 95%, respectively). We also identified streptococcin genes unique to 36% of the Gambian LIC isolates and a higher prevalence (48%) of glucuronic acid utilization pathway genes in the Gambian LIC isolates than in the Sheffield HIC isolates (26%). Comparison to a wider collection of HIC and LIC isolate genomes supported our findings of differing emm diversity and prevalence of bacterial factors. Our study provides insight into the genetics of LIC isolates and how they compare to HIC isolates. IMPORTANCE The global burden of rheumatic heart disease (RHD) has triggered a World Health Organization response to drive forward development of a vaccine against the causative human pathogen Streptococcus pyogenes. This burden stems primarily from low- and middle-income settings where there are high levels of S. pyogenes skin and soft tissue infections, which can lead to RHD. Our study provides much needed whole-genome-based molecular characterization of isolates causing skin infections in Sukuta, The Gambia, a low-income country (LIC) in West Africa where infection and RHD rates are high. Although we identified a greater level of diversity in these LIC isolates than in isolates from Sheffield, United Kingdom (a high-income country), there were some shared features. There were also some features that differed by geographical region, warranting further investigation into their contribution to infection. Our study has also contributed data essential for the development of a vaccine that would target geographically relevant strains.
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- 2023
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5. Effect of intra-partum azithromycin on the development of the infant nasopharyngeal microbiota: A post hoc analysis of a double-blind randomized trial
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Bakary Sanyang, Thushan I. de Silva, Abdoulie Kanteh, Abdoulie Bojang, Jarra Manneh, Wouter A.A. de Steenhuijsen Piters, Chikondi Peno, Debby Bogaert, Abdul Karim Sesay, and Anna Roca
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Azithromycin ,Intrapartum ,Infant ,Nasopharyngeal microbiota ,West Africa ,Medicine ,Medicine (General) ,R5-920 - Abstract
Summary: Background: Sepsis is a leading cause of neonatal death. Intrapartum azithromycin reduces neonatal nasopharyngeal carriage of potentially pathogenic bacteria, a prerequisite for sepsis. Early antibiotic exposure has been associated with microbiota perturbations with varying effects. This study aims to understand the effect of intrapartum azithromycin intervention on the developing nasopharyngeal microbiota of the child. Methods: Using 16S rRNA gene sequencing, we analysed the microbiota of 343 nasopharyngeal samples collected from birth to 12 months from 109 healthy infants selected from a double-blind randomized placebo-controlled clinical trial conducted in the Gambia (PregnAnZI-1). In the trial, 829 women were given 2g oral azithromycin or placebo (1:1) during labour with the objective of reducing bacterial carriage in mother and child during the neonatal period. The post-hoc analysis presented here assessed the effect of the intervention on the child nasopharyngeal microbiota development. Findings: 55 children were from mothers given azithromycin and 54 from mothers given placebo. Comparing arms, we found an increase in alpha-diversity at day-6 (p = 0·018), and a significant effect on overall microbiota composition at days 6 and 28 (R2 = 4.4%, q = 0·007 and R2 = 2.3%, q = 0·018 respectively). At genus level, we found lower representation of Staphylococcus at day-6 (q = 0·0303) and higher representation of Moraxella at 12 months (q = 0·0443). Unsupervised clustering of samples by microbial community similarity showed different community dynamics between the intervention and placebo arms during the neonatal period. Interpretation: These results indicate that intrapartum azithromycin caused short-term alterations in the nasopharyngeal microbiota with modest overall effect at 12 months of age. Further exploration of the effects of these variations on microbiome function will give more insight on the potential risks and benefits, for the child, associated with this intervention. Funding: This work was jointly funded by the Medical Research Council (UK) (MC_EX_MR/J010391/1/MRC), Bill & Melinda Gates Foundation (OPP1196513), and MRCG@LSHTM Doctoral Training Program.
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- 2022
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6. Evolution of the Ace-1 and Gste2 Mutations and Their Potential Impact on the Use of Carbamate and Organophosphates in IRS for Controlling Anopheles gambiae s.l., the Major Malaria Mosquito in Senegal
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Moussa Diallo, Ebrima SM Kolley, Abdoulaye Kane Dia, Mary Aigbiremo Oboh, Fatoumata Seck, Jarra Manneh, Abdul Karim Sesay, Seynabou Macote Diédhiou, Pape Cheikh Sarr, Ousmane Sy, Badara Samb, Oumar Gaye, Ousmane Faye, Lassana Konaté, Benoit Sessinou Assogba, and El Hadji Amadou Niang
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insecticide resistance ,Anopheles gambiae s.l. ,Ace-1 ,Gste2 ,evolution ,genetic diversity ,Medicine - Abstract
Widespread of insecticide resistance amongst the species of the Anopheles gambiae complex continues to threaten vector control in Senegal. In this study, we investigated the presence and evolution of the Ace-1 and Gste2 resistance genes in natural populations of Anopheles gambiae s.l., the main malaria vector in Senegal. Using historical samples collected from ten sentinel health districts, this study focused on three different years (2013, 2017, and 2018) marking the periods of shift between the main public health insecticides families (pyrethroids, carbamates, organophosphates) used in IRS to track back the evolutionary history of the resistance mutations on the Ace-1 and Gste2 loci. The results revealed the presence of four members of the Anopheles gambiae complex, with the predominance of An. arabiensis followed by An. gambiae, An. coluzzii, and An. gambiae–coluzzii hybrids. The Ace-1 mutation was only detected in An. gambiae and An. gambiae–coluzzii hybrids at low frequencies varying between 0.006 and 0.02, while the Gste2 mutation was found in all the species with a frequency ranging between 0.02 and 0.25. The Ace-1 and Gste2 genes were highly diversified with twenty-two and thirty-one different haplotypes, respectively. The neutrality tests on each gene indicated a negative Tajima’s D, suggesting the abundance of rare alleles. The presence and spread of the Ace-1 and Gste2 resistance mutations represent a serious threat to of the effectiveness and the sustainability of IRS-based interventions using carbamates or organophosphates to manage the widespread pyrethroids resistance in Senegal. These data are of the highest importance to support the NMCP for evidence-based vector control interventions selection and targeting.
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- 2022
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7. Translation of genomic epidemiology of infectious pathogens: Enhancing African genomics hubs for outbreaks
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Mary Aigbiremo Oboh, Semeeh Akinwale Omoleke, Olumide Ajibola, Jarra Manneh, Abdoulie Kanteh, Abdul-Karim Sesay, and Alfred Amambua-Ngwa
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COVID-19 ,Africa ,GISAID ,ACDC ,Genomic hubs ,Infectious and parasitic diseases ,RC109-216 - Abstract
Background: Deadly emerging infectious pathogens pose an unprecedented challenge to health systems and economies, especially across Africa, where health care infrastructure is weak, and poverty rates remain high. Genomic technologies are vital for enhancing the understanding and development of intervention approaches against these pathogens, including Ebola and the novel coronavirus disease 2019 (COVID-19). Discussion: Africa has contributed few genomes of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) to the global pool in growing open access repositories. To bridge this gap, the Africa Centre for Disease Control and Prevention (ACDC) is coordinating continent-wide initiatives to establish genomic hubs in selected well-resourced African centres of excellence. This will allow for standardisation and efficient and rapid data generation and curation. However, the strategy to ensure capacity for high-throughput genomics at selected hubs should not overshadow the deployment of portable, field-friendly and technically less demanding genomics technologies in all affected countries. This will enhance small-scale local genomic surveillance in outbreaks, leaving validation and large-scale approaches to be taken at central genomic hubs. Conclusion: The ACDC needs to scale-up its campaign for government support across African Union countries to ensure the sustainable financing of its strategy for increased pathogen genomic intelligence and other interventions in current and inevitable future epidemics in Africa.
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- 2020
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8. Origin of imported SARS-CoV-2 strains in The Gambia identified from whole genome sequences.
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Abdoulie Kanteh, Jarra Manneh, Sona Jabang, Mariama A Kujabi, Bakary Sanyang, Mary A Oboh, Abdoulie Bojang, Haruna S Jallow, Davis Nwakanma, Ousman Secka, Anna Roca, Alfred Amambua-Ngwa, Martin Antonio, Ignatius Baldeh, Karen Forrest, Ahmadou Lamin Samateh, Umberto D'Alessandro, and Abdul Karim Sesay
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Medicine ,Science - Abstract
The SARS-CoV-2 disease, first detected in Wuhan, China, in December 2019 has become a global pandemic and is causing an unprecedented burden on health care systems and the economy globally. While the travel history of index cases may suggest the origin of infection, phylogenetic analysis of isolated strains from these cases and contacts will increase the understanding and link between local transmission and other global populations. The objective of this analysis was to provide genomic data on the first six cases of SARS-CoV-2 in The Gambia and to determine the source of infection. This ultimately provide baseline data for subsequent local transmission and contribute genomic diversity information towards local and global data. Our analysis has shown that the SARS-CoV-2 virus identified in The Gambia are of European and Asian origin and sequenced data matched patients' travel history. In addition, we were able to show that two COVID-19 positive cases travelling in the same flight had different strains of SARS-CoV-2. Although whole genome sequencing (WGS) data is still limited in sub-Saharan Africa, this approach has proven to be a highly sensitive, specific and confirmatory tool for SARS-CoV-2 detection.
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- 2021
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9. Genomic epidemiology of SARS-CoV-2 infections in The Gambia, March 2020 to Jan 2022
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Abdoulie Kanteh, Haruna S. Jallow, Jarra Manneh, Bakary Sanyang, Mariama A. Kujabi, Sainabou Laye Ndure, Sheikh Jarju, Alhagie Papa Sey, Dabiri K Damilare, Yaya Bah, Sana Sambou, Gibril Jarju, Buba Manjang, Abubacarr Jagne, Sheikh Omar Bittaye, Mustapha Bittaye, Karen Forrest, Desta Alamerew Tiruneh, Ahmadou Lamin Samateh, Sheriffo Jange, Stéphane Hué, Nuredin Muhammed, Alfred Amambua-Ngwa, Beate Kampmann, Umberto D’Alessandro, Thushan I. de Silva, Anna Roca, and Abdul Karim Sesay
- Abstract
BackgroundCOVID-19, caused by SARS-CoV-2, is one of the deadliest pandemics over the last 100 years. Sequencing is playing an important role in monitoring the evolution of the virus, including the detection of new viral variants. This study describes the genomic epidemiology of SARS-CoV-2 infections in The Gambia.MethodsNasopharyngeal and/or oropharyngeal swabs collected from suspected cases and travellers were tested for SARS-CoV-2 using standard RT-PCR methods. SARS-CoV-2 positive samples were sequenced following standard library preparation and sequencing protocols. Bioinformatic analysis was done using ARTIC pipelines and lineages assigned using Pangolin.FindingsBetween March 2020 to January 2022, there were almost 12,000 SARS-CoV-2 confirmed cases distributed into four waves, each of them lasting between 4 weeks and 4 months, with more cases during the rainy seasons (July-October). As shown by the 1643 sequenced samples, each wave occurred after new viral variants and/or lineages were introduced in The Gambia, generally those already established in Europe and/or in other African countries. Local transmission was higher during the first and third wave, with mostly B.1.416/Senegal/Gambian lineage and AY.34.1/Delta subtype, respectively. The second wave was driven by two variants, namely Alpha and Eta and B.1.1.420 lineage. The Omicron/fourth wave was the shortest.InterpretationEfficient surveillance, including strengthening entry points and screening asymptomatic individuals especially during the rainy seasons would be important to promptly detect and control future waves in The Gambia and the subregion.FundingMedical Research Unit The Gambia at LSHTM, UK Research and Innovation funding (grant reference MC_PC_19084), MRC/UKRI MC_PC_19084 and World Health Organisation.
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- 2022
10. Evolution of the
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Moussa, Diallo, Ebrima Sm, Kolley, Abdoulaye Kane, Dia, Mary Aigbiremo, Oboh, Fatoumata, Seck, Jarra, Manneh, Abdul Karim, Sesay, Seynabou Macote, Diédhiou, Pape Cheikh, Sarr, Ousmane, Sy, Badara, Samb, Oumar, Gaye, Ousmane, Faye, Lassana, Konaté, Benoit Sessinou, Assogba, and El Hadji Amadou, Niang
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Widespread of insecticide resistance amongst the species of the
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- 2022
11. Simple and structured model to build sequencing capacity in west Africa
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Abdoulie Kanteh, Jarra Manneh, Bakary Sanyang, Mariama A Kujabi, Haruna S Jallow, Dabiri Damilare K, Sainabou Laye Ndure, and Abdul Karim Sesay
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Africa, Western ,Humans ,General Medicine ,Global Health - Published
- 2022
12. Comparative genomic analysis of skin and soft tissue Streptococcus pyogenes isolates from low- and high-income settings
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Jarra Manneh, Saikou Y. Bah, Abdul Karim Sesay, Roy R. Chaudhuri, Michael Marks, Henna Khalid, Alexander J Keeley, Elina Senghore, Edwin P. Armitage, Lisa Tilley, Saffiatou Darboe, Thushan I de Silva, and Claire E. Turner
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Tetracycline ,Biology ,Skin infection ,medicine.disease ,medicine.disease_cause ,Genome ,DNA sequencing ,Microbiology ,Human morbidity ,Streptococcus pyogenes ,medicine ,Gene ,Prophage ,medicine.drug - Abstract
Streptococcus pyogenes is a leading cause of human morbidity and mortality, especially in resource limited settings. The World Health Organisation has recently made a vaccine for S. pyogenes a global health priority to reduce the burden of the post-infection rheumatic heart disease. For a vaccine to be active against all relevant strains in each region, molecular characterisation of circulating S. pyogenes isolates is needed. We performed extensive comparative whole genome analyses of S. pyogenes isolates from skin and soft tissue infections in The Gambia, West Africa, where there is a high burden of such infections. To act as a comparator to this low-income country (LIC) collection of isolates, we performed genome sequencing of isolates from skin infections in Sheffield, UK, as representative high-income country (HIC) isolates. LIC isolates from The Gambia were genetically more diverse (46 emm-types in 107 isolates) compared to HIC isolates from Sheffield (23 emm-types in 142 isolates), with only 7 overlapping emm-types and with diverse genetic backgrounds. Characterisation of other molecular markers indicated some shared features, including a high prevalence of the skin infection-associated emm-pattern D and the variable fibronectin-collagen-T antigen (FCT) types FCT-3 and FCT-4. A previously unidentified FCT (FCT-10) was identified in the LIC isolates, belonging to two different emm-types. A high proportion (79/107; 73.8%) of LIC isolates carried genes for tetracycline resistance, compared to 53/142 (37.3%) HIC isolates. There was also evidence of different circulating prophages, as very few prophage-associated DNases and lower numbers of superantigens were detected in LIC isolates. Our study provides much needed insight into the genetics of circulating isolates in a LIC (The Gambia), and how they differ from those circulating in HICs (Sheffield, UK). Common molecular features may act as bacterial drivers for specific infection types, regardless of the diverse genetic background.
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- 2021
13. First detection of SARS-CoV-2 variant B.1.1.7 in Senegal
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B Ndiaye, Abdul Karim Sesay, Ambroise Ahoudi, Abdoulie Kanteh, Djibril Wade, Ndeye Coumba Toure-Kane, Umberto D'Alessandro, Aminata Dia, Moustapha Mbow, Jean Jacques Nsoumou Malomar, Cheikh Ibrahima Lo, Abdou Padane, Jarra Manneh, Souleymane Mboup, Papa Alassane Diaw, Astou Gueye-Gaye, Nafissatou Leye, Yacine Amet Dia, Gora Lo, Ndeye Diabou Diagne, and Aminata Mboup
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2019-20 coronavirus outbreak ,Coronavirus disease 2019 (COVID-19) ,SARS-CoV-2 ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,COVID-19 ,UK variant ,Infectious and parasitic diseases ,RC109-216 ,Microbiology ,Virology ,DNA sequencing ,Senegal ,genome sequencing ,Infectious Diseases ,Geography ,Editorial ,british variant ,Africa - Published
- 2021
14. Invasive atypical non-typhoidal Salmonella serovars in The Gambia
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Nabil-Fareed Alikhan, Rasheed Salaudeen, Yekini Olatunji, Andrew J. Page, Jarra Manneh, Grant A. Mackenzie, Abdul Karim Sesay, Usman N. Ikumapayi, and Abdoulie Kanteh
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Serotype ,Salmonella ,Population ,Virulence ,Pathogens and Epidemiology ,Biology ,Serogroup ,medicine.disease_cause ,Microbiology ,Antibiotic resistance ,Case fatality rate ,medicine ,Humans ,education ,Research Articles ,Africa South of the Sahara ,whole genome sequencing ,education.field_of_study ,atypical serovar ,Incidence (epidemiology) ,invasive non-typhoidal Salmonella ,General Medicine ,Salmonella Infections ,Gambia ,Gentamicin ,cytolethal distending toxin gene ,medicine.drug - Abstract
Invasive non-typhoidal Salmonella (iNTS) disease continues to be a significant public health problem in sub-Saharan Africa. Common clinical misdiagnosis, antimicrobial resistance, high case fatality and lack of a vaccine make iNTS a priority for global health research. Using whole genome sequence analysis of 164 invasive Salmonella isolates obtained through population-based surveillance between 2008 and 2016, we conducted genomic analysis of the serovars causing invasive Salmonella diseases in rural Gambia. The incidence of iNTS varied over time. The proportion of atypical serovars causing disease increased over time from 40 to 65 % compared to the typical serovars Enteritidis and Typhimurium that decreased from 30 to 12 %. Overall iNTS case fatality was 10%, but case fatality associated with atypical iNTS alone was 10 %. Genetic virulence factors were identified in 14/70 (20 %) typical serovars and 45/68 (66 %) of the atypical serovars and were associated with: invasion, proliferation and/or translocation (Clade A); and host colonization and immune modulation (Clade G). Among Enteritidis isolates, 33/40 were resistant to four or more of the antimicrobials tested, except ciprofloxacin, to which all isolates were susceptible. Resistance was low in Typhimurium isolates, but all 16 isolates were resistant to gentamicin. The increase in incidence and proportion of iNTS disease caused by atypical serovars is concerning. The increased proportion of atypical serovars and the high associated case fatality may be related to acquisition of specific genetic virulence factors. These factors may provide a selective advantage to the atypical serovars. Investigations should be conducted elsewhere in Africa to identify potential changes in the distribution of iNTS serovars and the extent of these virulence elements.
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- 2021
15. Origin of imported SARS-CoV-2 strains in The Gambia identified from Whole Genome Sequences
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Umberto D'Alessandro, Jarra Manneh, Ahmadou Lamin Samateh, Ousman Secka, Davis Nwakanma, Martin Antonio, Sona Jabang, Alfred Amambua-Ngwa, Abdul Karim Sesay, Bakary Sanyang, Mariama A. Kujabi, Ignatius Baldeh, Mary Aigbiremo Oboh, Abdoulie Kanteh, Haruna S. Jallow, Abdoulie Bojang, Karen Forrest, and Anna Roca
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RNA viruses ,Viral Diseases ,Pulmonology ,Library ,Coronaviruses ,Single Nucleotide Polymorphisms ,Genome ,law.invention ,Geographical Locations ,Medical Conditions ,law ,Pandemic ,Pathology and laboratory medicine ,Phylogeny ,Data Management ,Single-Stranded RNA ,Genetics ,Likelihood Functions ,Multidisciplinary ,Phylogenetic tree ,Phylogenetic Analysis ,Genomics ,Medical microbiology ,Phylogenetics ,Infectious Diseases ,Transmission (mechanics) ,Viruses ,Medicine ,Gambia ,SARS CoV 2 ,Pathogens ,Research Article ,Computer and Information Sciences ,China ,Asia ,SARS coronavirus ,Science ,Genome, Viral ,Biology ,Microbiology ,Virus ,Respiratory Disorders ,Complementary DNA ,Genetic variation ,Humans ,Evolutionary Systematics ,Taxonomy ,Medicine and health sciences ,Whole genome sequencing ,Evolutionary Biology ,Biology and life sciences ,Whole Genome Sequencing ,SARS-CoV-2 ,Organisms ,Viral pathogens ,COVID-19 ,Genetic Variation ,Covid 19 ,Microbial pathogens ,Evolutionary biology ,People and Places ,Africa ,Respiratory Infections ,Nanopore sequencing ,Reference genome - Abstract
The SARS-CoV-2 disease, first detected in Wuhan, China, in December 2019 has become a global pandemic and is causing an unprecedented burden on health care systems and the economy globally. While the travel history of index cases may suggest the origin of infection, phylogenetic analysis of isolated strains from these cases and contacts will increase the understanding and link between local transmission and other global populations. The objective of this analysis was to provide genomic data on the first six cases of SARS-CoV-2 in The Gambia and to determine the source of infection. This ultimately provide baseline data for subsequent local transmission and contribute genomic diversity information towards local and global data. Our analysis has shown that the SARS-CoV-2 virus identified in The Gambia are of European and Asian origin and sequenced data matched patients’ travel history. In addition, we were able to show that two COVID-19 positive cases travelling in the same flight had different strains of SARS-CoV-2. Although whole genome sequencing (WGS) data is still limited in sub-Saharan Africa, this approach has proven to be a highly sensitive, specific and confirmatory tool for SARS-CoV-2 detection.
- Published
- 2020
16. An outbreak of Serratia liquefaciens at a rural health center in The Gambia
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Grant A. Mackenzie, Modou Lamin, Abdoulie Kanteh, Usman N. Ikumapayi, and Jarra Manneh
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Male ,Isolation (health care) ,medicine.drug_class ,Attitude of Health Personnel ,media_common.quotation_subject ,Antibiotics ,030204 cardiovascular system & hematology ,Serratia liquefaciens ,Microbiology ,Disease Outbreaks ,Serratia Infections ,03 medical and health sciences ,0302 clinical medicine ,Professional Competence ,Hygiene ,Virology ,Environmental health ,Environmental Microbiology ,Medicine ,Infection control ,Humans ,030212 general & internal medicine ,Typing ,media_common ,Bacteriological Techniques ,Cross Infection ,business.industry ,Rural health ,Infant, Newborn ,Outbreak ,Infant ,General Medicine ,Infectious Diseases ,Child, Preschool ,Equipment Contamination ,Parasitology ,Female ,Gambia ,Rural Health Services ,business ,Drug Contamination - Abstract
Introduction: Healthcare-associated infections (HAIs) are better documented in developed than in developing countries. There are emerging reports regarding the high frequency of HAIs in developing countries. We aimed to report an outbreak of an HAI caused by Serratia liquefaciens at a rural health center in The Gambia. Methodology: Following an abrupt increase in the isolation of S. liquefaciens in clinical samples, laboratory and clinical consumables, as well as staff, were screened for contamination with S. liquefaciens. Conventional microbiological techniques and biochemical identification tests were used. A phenotypic typing was achieved using the Kirby-Bauer antibiotic susceptibility method. Strategies to control the outbreak were implemented. Results: A total of 794 samples were processed during the outbreak; 44 (6%) grew S. liquefaciens. Five (25%) of the 20 suspected contaminated materials (hospital consumables and equipment) screened yielded growth of the organism. The primary source of the outbreak was hospital consumables. Three (7%) of the 44 infected children died with no other known cause than S. liquefaciens infection. Ninety-nine percent similarity of the antibiogram phenotypic typing suggests the isolates were from the same clonal origin. The outbreak was successfully controlled after the removal and sterilization of the respective contaminated fluids and equipment. Conclusions: This HAI was caused by poor practice in the preparation of medications for nebulization and intravenous infusion, hygiene practices, and a lack of awareness among staff about infection control. We recommend further studies to delineate the role played by HAIs in the developing world.
- Published
- 2015
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