Biology subjects

Amoako, D. G.

Publications and source records attributed to Amoako, D. G..

9 recordsLinked to original sources

bioRxiv2025

Genomic and Bioinformatic Insights into Enterococcus faecalis from Retail Meats in Nigeria

BackgroundEnterococcus faecalis (E. faecalis) is a commensal and opportunistic pathogen increasingly recognized for its antimicrobial resistance (AMR) and zoonotic potential. This study employs whole-genome sequencing (WGS) to characterize E. faecalis isolates from retail meat samples, focusing on antimicrobial resistance genes (ARGs), virulence determinants, mobile genetic elements, and phylogenomic relationships. Materials and MethodsFifty raw meat samples, including chicken (n=18), beef (n=17), and turkey (n=15), were collected from retail markets in Akungba-Akoko, Nigeria. E. faecalis isolates were identified using standard microbiological methods and subjected to antimicrobial susceptibility testing were further analysed using WGS. ResultsTen E. faecalis isolates were recovered, with the highest prevalence in chicken (n=6), followed by beef (n=2) and turkey (n=2). All isolates were resistant to clindamycin, erythromycin, and tetracycline. Frequent ARGs included aac(6)-aph(2), ant(6)-Ia, lsa(A), erm(B), tet(M), and tet(L). Plasmid replicons rep9c and repUS43 showed ST-specific associations with ST477 and ST16, respectively. MGEs such as IS3, IS6, IS256, and IS1380 co-localized with ARGs and virulence determinants. Phylogenomic analysis revealed two major lineages, with ST477 distributed across meat types and ST16 restricted to chicken. Comparative genomic analysis with publicly available African E. faecalis isolates revealed distinct clonal lineages and geographic clustering across the continent. ConclusionThe co-occurrence of multidrug resistance, virulence factors, and MGEs in foodborne E. faecalis poses a public health concern due to the risk of horizontal gene transfer and zoonotic spread. These findings underscore the need for genomic surveillance and antimicrobial stewardship in food systems, particularly in low- and middle-income countries.

genomics↗

bioRxiv2024

Genomic characterization of foodborne Salmonella enterica and Escherichia coli isolates from Saboba district and Bolgatanga Municipality Ghana

Salmonella enterica and Escherichia coli are well-known bacteria commonly associated with foodborne illnesses in humans and animals. Genomic characterization of these pathogens provides valuable insights into their evolution, virulence factors and resistance determinants. This study aimed to characterized previously isolated Salmonella (n = 14) and E. coli (n = 19) from milk, meat and its associated utensils in Ghana using whole-genome sequencing. Most of the Salmonella serovars (Fresno, Plymouth, Infantis, Give and Orleans) identified in this study are yet to be reported in Ghana. Most Salmonella isolates were pan-sensitive, but genes conferring resistance to fosfomycin (fosA7.2) and tetracycline (tet(A)) were detected in one and three isolates, respectively. Seven of the Salmonella isolates carry the IncI1-I(Gamma) plasmid replicon. Although antimicrobial resistance was not common among Salmonella strains, most (11/19) of the E. coli strains had at least one resistance gene, with nearly half (8/19) being multidrug resistant and carrying mobile elements. Three of the 19 E. coli strains belong to serovars commonly associated with enteroaggregative E. coli (EAEC) pathotype. While strains belonging to virulence-associated lineages lacked key plasmid-encoded virulence plasmids, several plasmid replicons were detected in most of the E. coli (14/19) strains. Food contaminated with these pathogens can serve as a vehicle for disease transmission, posing a significant public health risk and necessitating stringent food safety and hygiene practices to prevent outbreaks. Hence, there is need for continuous surveillance and preventive measures to stop the spread of foodborne pathogens and reduce the risk of associated illnesses in Ghana.

microbiology↗

bioRxiv2024

Enable, Empower, Succeed: Harnessing Open Science for Antimicrobial Resistance Containment

Antimicrobial resistance (AMR) poses a significant threat to global health, particularly in Western sub-Saharan Africa where 27.3 deaths per 100,000 lives are affected, and surveillance and control measures are often limited. Genomics research plays a crucial role in understanding the emergence, spread and containment measures of AMR. However, its implementation in such settings is particularly challenging due to limited human capacity. This manuscript outlines a three-day bioinformatics workshop in Cameroon, highlighting efforts to build human capacity for genomics research to support AMR surveillance using readily accessible and user-friendly web-based tools. The workshop introduced participants to basic next-generation sequencing concepts, data file formats used in bacterial genomics, data sharing procedures and considerations, as well as the use of web-based bioinformatics software to analyse genomic data, including in silico prediction of AMR, phylogenetics analyses, and a quick introduction to Linux(C) command line. We provide a detailed description of the relevant training approaches used, including workshop structure, the selection and planning, and utilization of freely available web-based tools, and the evaluation methods employed. Our approach aimed to overcome limitations such as inadequate infrastructure, limited access to computational resources, and scarcity of expertise. By leveraging the power of freely available web-based tools, we demonstrated how participants can acquire fundamental bioinformatics skills, enhance their understanding of biological data analysis, and contribute to the field, even in an underprivileged environment. Our findings highlight the effectiveness of this training approach in empowering local researchers and bridging the bioinformatics gap in genomics surveillance of AMR in resource-constrained settings. Building human capacity for genomics research globally, and especially in resource-constrained settings, is imperative for ensuring global health and sustainable containment of AMR. Data summaryThe authors confirm that all supporting data, code and protocols have been provided within the article or through supplementary data files. Impact StatementAntimicrobial resistance (AMR) is a major global health threat, especially in Western sub-Saharan Africa, where 27.3 deaths per 100,000 lives occur. Genomics research play an instrumental role for understanding AMRs emergence, spread, and containment measures. However, its implementation in these settings is challenging due to limited human capacity. A three-day bioinformatics workshop in Cameroon aimed to build human capacity for genomics research using web-based tools. Participants were introduced to next-generation sequencing concepts, data file formats, data sharing procedures, and web-based bioinformatics software for analysing genomic data. The workshop aimed to overcome limitations like inadequate infrastructure, computational resources, and expertise scarcity. The findings show the effectiveness of this training approach in empowering local researchers and bridging the bioinformatics gap in genomics surveillance of AMR in resource-constrained settings.

scientific communication and education↗

bioRxiv2022

Molecular Dynamic Investigation of H5N1 Influenza Virus Dual H274Y-I222K Mutation Resistance to Peramivir

In light of the rapid rise of an influenza pandemic, the constant genetic mutations of H5N1 influenza viruses pose a threat. Mutations at the sialic site are often responsible for multiple drug resistance. To design effective new inhibitors, it is necessary to undertake research into the mechanism of resistance of influenza viruses and their rapid mutations. The molecular dynamic simulation technique has been an instrumental tool in understanding how proteins function from an atomic perspective. A thorough investigation has not been conducted using molecular dynamics to examine the impact of these mutations (I222K, H274Y, and H274Y-I222K) on Peramivir. This study investigates the effects of I222K, H274Y, H274Y-I222K substitution on the neuraminidase-Peramivir complex and identifies responsible residues for complex conformations. The mutations caused distorted Peramivir orientation in the enzyme active site, which affected the inhibitors binding. In the presence of various mutations, interaction between protein and ligand became less thermodynamically favorable. We observed the following trend in binding free energy difference: WT<I222<H274Y<H274Y-I222K. As a result of the thermodynamic instability of the mutant complexes, Peramivirs potency is reduced due to impaired binding interactions. Wild type complex displays thermodynamic stability and strong protein-ligand interactions due to their high total energy contributions and low residue flexibility. Based on the energy decomposition analysis, Arg117, Arg224, and Arg292 contributed the largest residual energy for the binding of Peramivir to wild type and mutants. These residues are thought to play a key role in the formation of the binding pocket between Peramivir and neuraminidase. This study provides a basis for investigating the effects of other mutations on Peramivirs efficacy against the H5N1 virus.

bioinformatics↗

bioRxiv2022

A molecular dynamic investigation of Human Rhinovirus 3C Protease Drug Target: Insights towards the design of potential Inhibitors

The 3C protease is distinguished from most proteases due to the presence of cysteine nucleophile that plays an essential role in viral replication. This peculiar structure encompassed with its role in viral replication has promoted 3C protease as an interesting target for therapeutic agents in the treatment of diseases caused by human rhinovirus (HRV). Herein we present a comprehensive molecular dynamics study of the comparison of two potent inhibitors, sg85 and rupintrivir complexed with HRV-3C protease. The binding free energy studies revealed a higher binding affinity for sg85 -58.853 kcal/mol than for rupintrivir -54.0873 kcal/mol and this was found to be in correlation with the experimental data. The energy decomposition analysis showed that, residues Leu 127, Thr 142, Ser 144, Gly 145, Tyr 146, Cys 147, His 161, Val 162, Gly 163, Gly 164, Asn 165, Phe 170 largely contributed to the binding of sg85, whereas His 40, Leu 127 and Gly 163 impacted the binding of rupintrivir. It further showed that His 40, Glu 71, Leu 127, Cys 147 Gly 163 and Gyl 164 are crucial residues that play a key role in ligand-enzyme binding; amongst these residues are residues of the conserved active site (His 40, Glu 71 and Cys 147). These findings provide a comprehensive understanding of the dynamics and structural features and will serve as guidance in the design and development of potent novel inhibitors of HRV. Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

bioinformatics↗

bioRxiv2022

Molecular mechanisms underlying Warburgia salutaris effects on oxidative stress and apoptotic parameters in Human Hepatoma Cells

This study aims to determine the molecular effects of Warburgia salutaris extract in HepG2 cells and elucidate the possible mechanisms. The MTT assay was employed to determine cell viability and the half maximal inhibitory concentration (IC50) of Warburgia salutaris-treated in HepG2 cells (0-5mg/ml). Extracellular lactate dehydrogenase and ATP were also quantified as a measure of cell viability. The production of reactive oxygen species (ROS) was assessed by quantifying lipid peroxidation and oxidative DNA damage, and reactive nitrogen species (RNS) in treated HepG2 cells. The cells response to free radicals was assessed by measuring GSH. Stress response antioxidant and apoptotic markers were detected using western blotting and /or qPCR. Cell death parameters assayed included annexin V, caspase activity and necrosis. Single-cell gel electrophoresis (SCGE) was used to visualise DNA damage in the HepG2 cells and confirmed with DNA fragmentation assay. The Hoechst assay allowed the visualisation of the nucleus to assess cell growth and apoptosis. Decreased cell viability was associated with a decreased level of ATP. The presence of oxidative stress was suggested by increased HSP70 and Nrf2 protein expression and confirmed by increase ROS, RNS, GPx and catalase; and a corresponding decrease of SOD2 and glutathione. Caspase 8 showed no significant difference between treatment concentrations, caspase 9 was decreased and caspase 3/7 increased. A reduction in p53 correlated with chromatin changes, increase in comet lengths and DNA fragmentation. NF{kappa}B protein was significantly decreased at the IC50, along with decreased cMyc protein expression. Our findings shows that Warburgia salutaris promotes apoptosis by inducing oxidative stress in HepG2 cells and may be a potential anti-cancer agent that would serve as an alternative to conventional therapeutic agents.

biochemistry↗

bioRxiv2022

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

Among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (i) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (ii) interactions of Spike with ACE2 receptors, and (iii) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any genomes within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron over all previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.

evolutionary biology↗

bioRxiv2018

In Vitro Potentiation of Carbapenems with Tannic Acid Against Carbapenemase Producing Enterobacteriaceae: Exploring Natural Products as Potential Carbapenemase Inhibitors

Resistance to antibiotics is increasing worldwide, necessitating urgent action to sustain the efficacy of existing antibiotics in clinical use. We show that tannic acid (TA) in combination with carbapenems can reduce and/or reverse the minimum inhibitory concentrations (MICs) of carbapenems to susceptible values in Enterobacteriaceae that express class A and B carbapenemases. MICs of carbapenems in the presence and absence of TA and other efflux pump inhibitors, TA-carbapenemases inhibition assays and computational studies were undertaken to determine the effect of TA on carbapenem susceptibility in Enterobacteriaceae. TA had the greatest effect on metallo-{beta}-lactamases (MBLs) followed by class A serine-{beta}-lactamases (SBLs). Antibiotic susceptibility testing showed that TA reversed the MICs of MBLs to susceptible values whilst substantially reducing the MICs of SBLs (class A). Tolerable cytotoxicity effect was observed for the concentrations tested. TA inhibited enzymes with a marked difference between {approx}50% inhibition (IC50) for NDM-1 and KPC-2. Computational studies including molecular docking, molecular dynamics simulations and binding free energy calculations showed that TA interact with both MBLs and SBLs hydrophobic sites. Moreover, TA had a stronger binding affinity for MBLs than SBLs as the MBLs, specifically VIM-1 and NDM-1, interact with a larger number of their catalytic active-site residues than that of OXA- 48 and KPC-2. These in vitro evaluations together with computational simulation explain the potentiating effect of TA toward carbapenems against carbapenem-resistance enterobacteriaceae. This study proposes TA as a promising adjuvant for MBLs and SBLs.

microbiology↗

bioRxiv2018

Evaluation of 1, 4, 7-Triazacyclononane (TACN) as a potential Metallo-B-Lactamase inhibitor in Enterobacteriaceae: Restoring the Activity of B-lactams

Metallo-{beta}-lactamase producing Enterobacteriaceae are of grave clinical concern particularly as there are no Metallo-{beta}-lactamase (MBL) inhibitors approved for clinical use. The discovery and development of MBL inhibitors to restore the efficacy of available {beta}-lactams are thus imperative. We investigated a zinc-chelating moiety, 1, 4, 7-triazacyclononane (TACN) for its inhibitory activity against clinical carbapenem-resistant Enterobacteriaceae. Minimum inhibitory concentrations (MICs), minimum bactericidal concentrations (MBCs), serum effect, fractional inhibitory concentrations index and time-kill kinetics were performed using broth microdilution techniques according to the Clinical Laboratory Standard Institute (CSLI) guidelines. Enzyme kinetic parameters and cytotoxicity effects of TACN were determined using spectrophotometric assays. The interactions of the enzyme-TACN complex were investigated by computational studies. Meropenem regained its activity against carbapenemase-producing Enterobacteriaceae, with the MIC decreasing to 0.03 mg/L in the presence of TACN. TACN-Meropenem combinations showed bactericidal effects with MIC/MBC ratio of [≤]4, and synergistic activity was observed. Human serum effects on the MICs were insignificant, and TACN was found to be non-cytotoxic at concentrations above the MIC values. Computational studies predicted that TACN inhibits MBLs by targeting their catalytic active site pockets. This was supported by its inhibition constant Ki = 0.044 {micro}M and inactivation constant kinact= 0.0406 (min-1) demonstrating that TACN inhibits MBLs efficiently and holds promise as a potential inhibitor.\n\nImportanceCarbapenem-resistant Enterobacteriaceae (CRE)-mediated infections remain a significant public health concern and have been reported as critical in the World Health Organizations Priority Pathogens List for the Research and Development of New Antibiotics. CRE produce enzymes such as Metallo-{beta}-lactamases (MBLs), which inactivate {beta}-lactam antibiotics. Combination therapies involving a {beta}-lactam antibiotic and a {beta}-lactamase inhibitor remain a major treatment option for infections caused by {beta}-lactamase-producing organisms. Currently, no MBL inhibitor-{beta}-lactam combination therapy is clinically available for MBL-positive bacterial infections. Hence, developing efficient molecules capable of inhibiting these enzymes could be a promising way to overcome this phenomenon. TACN played a significant role in the inhibitory activity of the tested molecules against CREs by potentiating the carbapenem. This study demonstrated that TACN inhibits MBLs efficiently and holds promises as a potential MBLs inhibitor to help curb the global health threat posed by MBL-producing CREs.

microbiology↗