Biology subjects

Osei Sekyere, J.

Publications and source records attributed to Osei Sekyere, J..

6 recordsLinked to original sources

bioRxiv2024

Molecular and Pathological Characterization of Cervicovaginal Specimens Evince Significant Protection Against HPV Infections, Bacterial Vaginosis, and Epithelial Cell Abnormalities by Lactobacillus species

BackgroundBacterial vaginosis (BV) results in dysbiosis in the vaginal microbiome and facilitates secondary human papilloma virus (HPV) infections, which can cause cervical abnormalities. The effects of Lactobacilli on BV-HPV infections and cervicovaginal pathology were investigated. MethodElectronic molecular and cytology laboratory results, and demographic records of 19,105 females screened for BV, HPV, and cervical cancer between August 2021 and April 2023 were collected. After data cleaning and reorganization, 15, 607 sample results were used. The data was subjected to epidemiological, statistical, and machine learning analyses to identify patterns, correlations, associations, and interactive effects of age, State, Lactobacilli, BV-associated pathogens, high-risk HPV (hrHPV) genotypes, BV, and cervical cytology. ResultsThe final dataset comprised of data from anonymized females (n = 15541, 99.57%), males (n = 13, 0.08%) and unknown gender (n = 53, 0.34%) between 14 and 95 years from 32 States and Washington D.C. Most samples were BV positive (n = 8282, 53.07%) and/or NILM (n = 11749) followed by 14.29% ASCUS (n = 2231), 7.14% LSIL (n = 1115), 1.04% RCC (n = 163), 0.53% HSIL (n = 82), 0.39% ASC-H (n = 61), and 0.16% AGC (n = 25). HPV-positive samples had higher BV pathogens and BV-positive diagnosis (between 51.90% and 68.60%) than BV-negative diagnosis. Lactobacillus gasseri (79.75%), Lactobacillus jensenii (82.68%), Lactobacillus crispatus (90.91%) were mostly found in BV-negative and NILM specimens. BV and ECA outcomes were significantly associated with age and State. Statistical, correlation, and machine learning models predictively confirmed these findings. ConclusionL. crispatus, followed by L. gasseri and L. jensenii, significantly maintains a healthy cervicovaginal microbiome by inhibiting harmful bacterial pathogens and high-risk HPV subtypes; L. iners have an opposing or neutral effect. Lay summary/importance/highlightsBacterial vaginosis (BV) and human papillomavirus (HPV) infections mostly occur in sexually active and reproductive-age women, adversely affecting their quality of life and predisposing them to sequelae of reproductive disorders. In this study, the protective effects of Lactobacilli against BV and HPV infections to maintain a healthy cervicovaginal microbiome were investigated. Lactobacillus crispatus, L. gasseri, and L. jensenii were common in clinical specimens that had no or relatively lower concentrations of hrHPV, BV, and cervico-vaginal cell abnormalities and vice versa. This shows how important these Lactobacilli are in maintaining a healthy cervix and vagina. Age and BV were found to be strongly associated with the incidence of HPV infections and epithelial cell abnormalities (ECAs). Some States had higher prevalence of BV and ECAs than others. Co-infection with multiple hrHPV and/or hrHPV-BV pathogens segued into negative health effects; some interactions were beneficial for the microbiome, albeit those were few. This makes multiple HPV genotype infections dangerous.

pathology↗

bioRxiv2024

Plasmid-borne mcr-1 and Replicative Transposition of Episomal and Chromosomal blaNDM-1, blaOXA-69, and blaOXA-23 Carbapenemases in a Clinical Acinetobacter baumannii Isolate

BackgroundA multidrug-resistant clinical A. baumannii isolate with resistance to most antibiotics was isolated from a patient at an intensive care unit. The genetic environment, transcriptome, mobile, and resistome were characterized. MethodThe MicroScan system, disc diffusion, and broth microdilution were used to determine the resistance profile of the isolate. A multiplex PCR assay was also used to screen for carbapenemases and mcr-1 to -5 resistance genes. Efflux-pump inhibitors were used to evaluate efflux activity. The resistome, mobilome, epigenome, and transcriptome were characterized. Results & conclusionThere was phenotypic resistance to 22 of the 25 antibiotics tested, intermediate resistance to levofloxacin and nalidixic acid, and susceptibility to tigecycline, which corresponded to the 27 resistance genes found in the genome, most of which occurred in multiple copies through replicative transposition. A plasmid-borne (pR-B2.MM_C3) mcr-1 and chromosomal blaPER-7, blaOXA-69, blaOXA-23 (three copies), blaADC-25, blaTEM-1B, and blaNDM-1 were found within composite transposons, ISs, and/or class 1 and 2 integrons on genomic islands. Types I and II methylases and restriction endonucleases were in close synteny to these resistance genes within the genomic islands; chromosomal genomic islands aligned with known plasmids. There was a closer evolutionary relationship between the strain and global strains but not local or regional strains; the resistomes also differed. Significantly expressed/repressed genes (6.2%) included resistance genes, hypothetical proteins, mobile elements, methyltransferases, transcription factors, membrane and efflux proteins. The genomic evolution observed in this strain explains its adaptability and pandrug resistance and shows its genomic plasticity on exposure to antibiotics.

genomics↗

bioRxiv2023

Genomic, Epigenomic, and Transcriptional Characterisation of Carbapenem and Colistin Resistance Mechanisms in Klebsiella pneumoniae and Enterobacter species.

The emergence of colistin and carbapenem-resistant Klebsiella pneumoniae isolates presents a significant global health threat. This study investigates the resistance mechanisms in six K. pneumoniae and four Enterobacter sp. isolates lacking carbapenemases or mcr genes using genomics and transcriptomics. The ten isolates were classified into three categories: non-carbapenemase-producing, carbapenem-resistant strains (n = 4), non-mcr-producing colistin-resistant strains (n = 5), and one isolate susceptible to both antibiotics. The analysis included phenotypic characterization using MicroScan ID/AST, enzyme (MCR and Metallo {beta}-lactamase) and efflux pump inhibition (EPI) assays. Whole-genome sequencing, RNA sequencing, and bioinformatics tools were employed in subsequent analysis. Most of the K. pneumoniae were ST307 with KL102 and O1/O2V2 serotypes. MicroScan revealed multidrug resistance, and AMR analysis identified numerous ARGs in K. pneumoniae. Enterobacter species possessed fewer resistance genes; nevertheless, they encoded virulence factors and gene mutations, potentially impacting the AST profile. K. pneumoniae ARGs were mainly plasmid-borne, with IncFIB(K)/IncFII(K) in Kp_15 harbouring up to nineteen ARGs. Virulence factors included biofilm formation, capsule production, and type IV secretion. Epigenomic investigations revealed prevalent type I (M1.Ecl34977I) and type II (M.Kpn34618Dcm) restriction modification sites. Compared to international isolates, the study isolates phylogenetically clustered more closely with Chinese strains. Transcriptomics showed high efflux pump activity in carbapenem-resistant isolates, confirmed by EPI. Further, mutations were identified in outer membrane proteins. Colistin-resistant isolates exhibited high capsule production, efflux pump, and putative glycotransferase activity, potentially influencing their phenotypes. In conclusion, genomic and transcriptional analyses enhanced our understanding of adaptive mechanisms in clinical multidrug-resistant pathogens, posing significant public health challenges.

molecular biology↗

bioRxiv2021

Pathogens, Virulence and Resistance Genes Surveillance with Metagenomics Can Pre-empt Dissemination and Escalation of Untreatable Infections: A Systematic Review and Meta-analyses.

BackgroundThe dissemination of pathogens carrying genetic elements such as antimicrobial resistance genes (ARGs), mobile-genetic elements (MGEs), virulome and methylome have a negative impact on food and environment safety, water quality and animal and human health. The applications of metagenomics to monitor and identify the prevalence/endemicity and emergence of these pathogenic agents from different sources were examined. MethodsArticles published in English language up to October 2020 were searched for on PubMed. Qualitative and quantitative data extracted from the included articles were translated into charts and maps. GraphPad Prism 9.0.2 was used to undertake statistical analysis using descriptive and column statistics, Chi-square, ANOVA, Wilcoxons signed-rank, and one-sample t-test. ResultsIn all, 143 articles from 39 countries from Europe, America, Asia, and Africa were quantitatively analysed. Metagenomes from sewage/wastewater, surface water samples (ocean, sea, river lake, stream and tap water), WWTP, effluents and sludge samples contained pathogenic bacteria (Aeromonas, Acinetobacter, Pseudomonas, Streptococcus, Bacteroides, Escherichia coli, Salmonella enterica, Klebsiella pneumoniae and Acinetobacter baumannii), viruses (Adenovirus, Enterovirus, Hepatovirus, Mamastrovirus and Rotavirus) and parasites (Acanthamoeba, Giardia, Entamoeba, Blastocystis and Naegleria). Integrons, plasmids, transposons, insertion sequences, prophages and integrative and conjugative elements were identified. ARGs mediating resistance to important antibiotics, including {beta}-lactams, aminoglycosides, fluoroquinolones, and tetracycline, and virulence factors such as secretion system, adherence, antiphagocytosis, capsule, invasion, iron uptake, hemolysin, and flagella. ConclusionClinically important pathogens, ARGs, and MGEs were identified in diverse clinical, environmental, and animal sources through metagenomics, which can be used to determine the prevalence and emergence of known and unknown pathogens and ARGs. Importance/significanceGlobal metagenomic analyses of drinking water, effluents, influents, un/-treated sewage, WWTPs, sludge, rivers, lakes, soil, sediments, biosolid, air and plants. showed the global distribution of diverse clinically important ARGs on mobile genetic elements, antimicrobial-resistant bacteria (ARB) and pathogens, metal resistance genes, and virulence genes in almost all environments. These depict the importance of shot-gun metagenomics as a surveillance tool for AMR and infectious disease control to safeguard water & food quality as well as public health from water- and food-borne outbreaks of pathogenic and ARB infections. More concerning was the identification of ARGs to last-resort antibiotics i.e., carbapenems, colistin, & tigecycline.

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↗

bioRxiv2018

The Molecular Epidemiology and Mechanisms of Antibiotic Resistance in Gram-positive Bacteria in Africa: A Systematic Review and Meta-Analysis from a One Health Perspective

A systematic review and meta-analysis of antibiotic-resistant Gram-positive bacteria in Africa, showing the molecular epidemiology of resistant species from animal, human and environmental sources, is lacking. Thus, the current burden, type, and sources of Gram-positive bacterial resistance and their dissemination routes from farm to fork is absent. To fill this One Health information gap, we systematically searched PubMed, Web of Science and African Journals Online for English research articles reporting on the resistance mechanisms and clonality of resistant Gram-positive bacteria in Africa within 2007 to 2018. The review and all statistical analysis were undertaken with 130 included articles.\n\nFrom our analyses, the same resistant Gram-positive bacterial clones, resistance genes, and mobile genetic elements (MGEs) are circulating in humans, animals and the environment. The resistance genes, mecA, erm(B), erm(C), tet(M), tet(K), tet(L), vanB, vanA, vanC, and tet(O), were found in isolates from humans, animals and the environment. Commonest clones and mobile genetic elements identified from all three sample sources included Staphylococcus aureus ST5 (n=208 isolates), ST 8 (n=116 isolates), ST 80 (n=123 isolates) and ST 88 (n=105 isolates), and IS16 (n=18 isolates), Tn916 (n=60 isolates) and SCCmec (n=202 isolates). Resistance to penicillin (n=4 224 isolates, 76.2%), erythromycin (n=3 552 isolates, 62.6%), ampicillin (n=1 507 isolates, 54.0%), sulfamethoxazole/trimethoprim (n=2 261 isolates, 46.0%), tetracycline (n=3 054 isolates, 42.1%), vancomycin (n=1 281 isolates, 41.2%), streptomycin (n=1 198 isolates, 37.0%), rifampicin (n=2 645 isolates, 33.1%), ciprofloxacin (n=1 394 isolates, 30.5%), clindamycin (n=1 256 isolates, 29.9%) and gentamicin (n=1 502 isolates, 27.3%) (p-value <0.0001) were commonest.\n\nMean resistance rates of 14.2% to 98.5% were recorded in 20 countries within the study period, which were mediated by clonal, polyclonal and horizontal transmission of resistance genes. A One Health approach to research, surveillance, molecular epidemiology, and antibiotic stewardship to contain ABR should be prioritized.

microbiology↗