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Otchere, I. D.

Publications and source records attributed to Otchere, I. D..

8 recordsLinked to original sources

Upper respiratory tract bacterial microbiome features associated with Streptococcus pneumoniae colonisation, environmental and demographic factors among older children in a rural setting in The Gambia

Abstract The upper respiratory tract (URT) microbiome plays a vital role in respiratory health, with older children (5-14 years old) serving as key reservoirs for the transmission of bacteria to younger individuals (< 5 years old). However, the URT microbiome in this age group remains poorly characterised, particularly in relation to colonisation by the pathobiont Streptococcus pneumoniae. To address this gap, we analysed URT samples collected over eight visits from 134 healthy children aged 5-14 years in The Gambia, using culture-dependent methods to detect S. pneumoniae and culture-independent 16S rRNA sequencing to characterise the microbiome in parallel. 16S rRNA sequencing identified Streptococcus and Prevotella as the dominant microbiome constituents. When integrating longitudinal sampling data, we observed temporal instability with frequent switches in microbiome profiles over time. URT samples colonised with S. pneumoniae were associated with increased abundance of Moraxella, Streptococcus and Haemophilus, whereas non-colonised URT samples were enriched with Granulicatella and Filifactor. S. pneumoniae colonisation was also associated with lower Shannon diversity compared with non-colonised samples. Age and season were the strongest determinants of microbiome composition; increasing age was associated with decreasing prevalence and abundance of taxa including Haemophilus and Moraxella, while gram-positive taxa were predominantly enriched in the dry season. These findings provide new insight into the URT microbiome of older children in The Gambia and highlight Granulicatella and Filifactor as potential contributors to colonisation resistance against S. pneumoniae.

microbiology↗

Potential benefits of Soymilk-burkina (Agbenu) consumption on gut health of women of reproductive age

BackgroundGut microbiome plays a crucial role in human health. This study investigated the impact of two soy-based foods, soymilk-burkina (SMB), a traditional fermented Ghanaian beverage) and soymilk-millet blend (SMMB), on the gut microbiome of women of reproductive age. MethodsFecal samples were collected from two cohorts of women consuming either SMB or SMMB soymilk-burkina or a soymilk-millet blend) at 2 weeks pre-intervention, baseline, during an 8-week intervention, and 4 weeks post-intervention. 16S rRNA gene amplicon sequencing was used to analyze the composition and diversity of the gut microbiome. Results{beta}-diversity analysis revealed no significant differences in overall community composition between the two cohorts. -diversity indices (Chao1, Shannon, Simpson) showed no significant differences in richness, evenness, or diversity between cohorts, suggesting a balanced gut ecosystem after both interventions. However, 20 dominant bacterial species were identified, including both beneficial (e.g., Faecalibacterium prausnitzii and Bacteroides vulgatus) and potentially harmful (e.g., Eubacterium rectale and Bacteroides fragilis) taxa. Soymilk-burkina consumption of soymilk-burkina significantly reduced the abundance of Eubacterium rectale (associated with colon cancer) and increased the abundance of F. prausnitzii (beneficial), suggesting potential gut health benefits. However, these effects were transient, highlighting the need for sustained dietary interventions. ConclusionThis study provides insights into the dynamic interplay between diet and the gut microbiome, particularly in the context of traditional fermented foods such as soymilk-burkina. Although short-term changes were observed, the long-term benefits may require consistent consumption. Further research is required to explore the mechanisms underlying these effects and their implications on broader health outcomes. Plain Language SummaryThe human body, particularly the gastrointestinal tract, hosts trillions of microorganisms, predominantly bacteria. These "gut microbes" play a crucial role in nutrient digestion, vitamin synthesis, and disease prevention. Dietary intake can significantly alter the composition of these microbial communities. This study investigated whether a traditional fermented beverage, soymilk-burkina, could enhance the gut health of women in Ghana. A comparative unfermented soymilk-millet blend was also examined. Forty women were randomly assigned to two groups, each consuming one of the soy beverages daily for an eight-week period. Fecal samples were collected at baseline, during, and after the intervention to analyze bacterial profiles. The results indicated no dramatic overall changes in the diversity or types of gut bacteria between the two groups. However, women who consumed fermented soymilk-burkina exhibited notable shifts, specifically a reduction in Eubacterium rectale, a bacterium associated with colon cancer, and an increase in beneficial Faecalibacterium prausnitzii, known for its positive impact on gut health. These positive alterations, however, appeared to be transient. Approximately one month after discontinuing the fermented product, the participants gut bacterial levels began reverting to their pre-study states. In conclusion, this study suggests that fermented soymilk-burkina may offer short-term benefits to gut health by promoting beneficial bacteria and reducing potentially harmful ones. Nevertheless, sustained consumption of this beverage is necessary to maintain these benefits. This research underscores the influence of diet on gut microbiota and highlights the potential of traditional fermented foods like soymilk-burkina for further exploration, although more research, particularly concerning long-term effects, is warranted.

microbiology↗

Phylogenetic population structure and drug resistance of Mycobacterium tuberculosis complex in the Volta Region of Ghana

ContextAvailable molecular epidemiological data from recent studies suggest significant genetic variation between the different phylogenetic lineages of Mycobacterium tuberculosis complex (MTBC) and the MTBC lineages might have adapted to different human populations AimThis study sought to determine the phylogenetic population structure of clinical MTBC isolates from the Volta Region of Ghana. MethodsThe MTBC isolates obtained from collected sputum samples were characterized by standard methods. Non-tuberculous mycobacterial isolates were characterized by amplification of the heat shock protein 65 (hsp65) gene and sequencing. The drug susceptibility profiles of the MTBCs determined using GenoType MTBDRplus ResultsOne hundred and seventeen (117, 93.6%) out of 125 mycobacterial positive isolates were characterized as members of the MTBC of which M. tuberculosis sensu stricto (MTBss) and M. africanum (Maf) were respectively 94 (80.3%) and 23 (19.7%). In all, 39 distinct spoligotype patterns were obtained; 26 for MTBss and 13 for Maf lineages. Spoligotyping identified 89 (76.04 %) Lineage 4, 16 (13.7 %) Lineage 5, 7 (6.0%) Lineage 6, 3 (2.6%) Lineage 2, 1(0.9%) Lineage 3 and 1 (0.9%) Lineage 1. Among the Lineage 4 isolates, 62/89 (69.7%) belonged to Cameroon sub-lineage, 13 (14.6%) Ghana, 8 (9.0%) Haarlem, 2 (2.2%) LAM, 1 (1.1%) Uganda I, 1 (1.1%) X and the remaining two were orphan. Significant localization of Maf was found within the Ho municipality (n=13, 29.5%) compared to the more cosmopolitan Ketu-South/Aflao (n=3, 8.3%) (p-value= 0.017). Eight (8) non-tuberculous mycobacteria were characterized as M. abscessus (7) and M. fortuitum (1) ConclusionWe confirmed the importance of M. africanum lineages as a cause of TB in the Volta region of Ghana. Key MessageThe phylogenetic population structure obtained agrees with previously described prevalence of M. tuberculosis complex phylogenetic lineages from other regions of Ghana. It also confirms the stable prevalence of M. africanum as an important human TB causing pathogen in Ghana.

microbiology↗

Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity

Pathogens of the Mycobacterium tuberculosis complex (MTBC) are considered monomorphic, with little gene content variation between strains. Nevertheless, several genotypic and phenotypic factors separate the different MTBC lineages (L), especially L5 and L6 (traditionally termed Mycobacterium africanum), from each other. However, genome variability and gene content especially of L5 and L6 strains have not been fully explored and may be potentially important for pathobiology and current approaches for genomic analysis of MTBC isolates, including transmission studies. We compared the genomes of 358 L5 clinical isolates (including 3 completed genomes and 355 Illumina WGS (whole genome sequenced) isolates) to the L5 complete genomes and H37Rv, and identified multiple genes differentially present or absent between H37Rv and L5 strains. Additionally, considerable gene content variability was found across L5 strains, including a split in the L5.3 sublineage into L5.3.1 and L5.3.2. These gene content differences had a small knock on effect on transmission cluster estimation, with clustering rates influenced by the selection of reference genome, and with potential over-estimation of recent transmission when using H37Rv as the reference genome. Our data show that the use of H37Rv as reference genome results in missing SNPs in genes unique for L5 strains. This potentially leads to an underestimation of the diversity present in the genome of L5 strains and in turn affects the transmission clustering rates. As such, a full capture of the gene diversity, especially for high resolution outbreak analysis, requires a variation of the single H37Rv-centric reference genome mapping approach currently used in most WGS data analysis pipelines. Moreover, the high within-lineage gene content variability suggests that the pan-genome of M. tuberculosis is at least several kilobases larger than previously thought, implying a concatenated or reference-free genome assembly (de novo) approach may be needed for particular questions. Data summarySequence data for the Illumina dataset are available at European Genome-phenome Archive (EGA; https://www.ebi.ac.uk/ega/) under the study accession numbers PRJEB38317 and PRJEB38656. Individual runs accession numbers are indicated in Table S8. PacBio raw reads for the L5 Benin genome are available on the ENA accession SAME3170744. The assembled L5 Benin genome is available on NCBI with accession PRJNA641267. To ensure naming conventions of the genes in the three L5 genomes can be followed, we have uploaded these annotated GFF files to figshare at https://doi.org/10.6084/m9.figshare.12911849.v1. Custom python scripts used in this analysis can be found at https://github.com/conmeehan/pathophy.

genetics↗

Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history

Human tuberculosis is caused by members of the Mycobacterium tuberculosis Complex (MTBC). The MTBC comprises several human-adapted lineages known as M. tuberculosis sensu stricto as well as two lineages (L5 and L6) traditionally referred to as M. africanum. Strains of L5 and L6 are largely limited to West Africa for reasons unknown, and little is known on their genomic diversity, phylogeography and evolution. Here, we analyzed the genomes of 365 L5 and 326 L6 strains, plus five related genomes that had not been classified into any of the known MTBC lineages, isolated from patients from 21 African countries. Our population genomic and phylogeographical analyses show that the unclassified genomes belonged to a new group that we propose to name MTBC Lineage 9 (L9). While the most likely ancestral distribution of L9 was predicted to be East Africa, the most likely ancestral distribution for both L5 and L6 was the Eastern part of West Africa. Moreover, we found important differences between L5 and L6 strains with respect to their phylogeographical substructure, genetic diversity and association with drug resistance. In conclusion, our study sheds new light onto the genomic diversity and evolutionary history of M. africanum, and highlights the need to consider the particularities of each MTBC lineage for understanding the ecology and epidemiology of tuberculosis in Africa and globally.

genomics↗

Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana

BackgroundBovine tuberculosis (bTB) caused by Mycobacterium bovis is a re-emerging problem in both livestock and humans. The association of some M. bovis strains with hyper-virulence, MDR-TB and disseminated disease makes it imperative to understand the biology of the pathogen.\n\nMethodsMycobacterium bovis (15) among 1755 M. tuberculosis complex (MTBC) isolated between 2012 and 2014 were characterized and analyzed for associated patient demography and other risk factors. Five of the M. bovis were whole-genome sequenced and comparatively analyzed against a global collection of published M. bovis genomes.\n\nResultsMycobacterium bovis was isolated from 3/560(0.5%) females and 12/1195(1.0%) males with pulmonary TB. The average age of M. bovis infected cases was 46.8 years (7-72years). TB patients from the Northern region of Ghana (1.9%;4/212) had a higher rate of infection with M. bovis (OR=2.7,p=0.0968) compared to those from the Greater Accra region (0.7%;11/1543). Among TB patients with available HIV status, the odds of isolating M. bovis from HIV patients (2/119) was 3.3 higher relative to non-HIV patients (4/774). Direct contact with livestock or their unpasteurized products was significantly associated with bTB (p<0.0001,OR=124.4,95% CI=30.1-508.3). Two (13.3%) of the M. bovis isolates were INH resistant due to the S315T mutation in katG whereas one (6.7%) was RIF resistant with Q432P and I1491S mutations in rpoB. M. bovis from Ghana resolved as mono-phyletic branch among mostly M. bovis from Africa irrespective of the host and were closest to the root of the global M. bovis phylogeny. M. bovis-specific amino acid mutations were detected among MTBC core genes such as mce1A, mmpL1, pks6, phoT, pstB, glgP and Rv2955c. Additional mutations P6T in chaA, G187E in mgtC, T35A in Rv1979c, S387A in narK1, L400F in fas and A563T in eccA1 were restricted to the 5 clinical M. bovis from Ghana.\n\nConclusionOur data indicate potential zoonotic transmission of bTB in Ghana and hence calls for intensified public education on bTB, especially among risk groups.

microbiology↗

Reduced transmission of Mycobacterium africanum compared to Mycobacterium tuberculosis in urban West Africa

BackgroundUnderstanding transmission dynamics is useful for tuberculosis (TB) control. We conducted a population-based molecular epidemiological study to understand TB transmission in Ghana.\n\nMethodsMycobacterium tuberculosis complex (MTBC) isolates obtained from prospectively-sampled pulmonary TB patients between July, 2012 and December, 2015 were confirmed as MTBC using IS6110 PCR. MTBC lineages were identified by large sequence polymorphism and single nucleotide polymorphism assays and further characterized using spoligotyping and standard 15-loci MIRU-VNTR typing. We used the n-1 method to estimate recent TB transmission and identified associated risk factors using logistic regression analysis.\n\nFindingsOut of 2,309 MTBC isolates, we identified 1,082 (46{middle dot}9%) single cases with 1,227 (53{middle dot}1%) isolates belonging to one of 276 clustered cases (clustering range; 2-35). Recent TB transmission rate was estimated to be 41{middle dot}2%. While we see no significant difference in the recent transmission rates between lineages of Mycobacterium africanum (lineage-5 (31{middle dot}8%); lineage-6 (24{middle dot}7%), p=0{middle dot}118), we found that lineage-4 belonging to the M. tuberculosis transmitted significantly higher (44{middle dot}9%, p<0{middle dot}001). Finally, apart from age being significantly associated with recent TB transmission (p=0{middle dot}007), we additionally identified a significant departure in the male/female ratio among very large clustered cases compared to the general TB patient population (3:1 vs. 2:1, p=0{middle dot}022).\n\nInterpretationsOur findings indicate high recent TB transmission suggesting occurrences of unsuspected outbreaks. The observed reduced transmission rate of M. africanum suggests other factor(s) may be responsible for its continuous presence in West Africa.\n\nFundingWellcome Trust Intermediate Fellowship Grant 097134/Z/11/Z to Dorothy Yeboah-Manu.

epidemiology↗

Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests different ecological niches

Mycobacterium africanum (Maf) causes up to half of human tuberculosis in West Africa, but little is known on this pathogen. We compared the genomes of 253 Maf clinical isolates from Ghana, including both L5 and L6. We found that the genomic diversity of L6 was higher than in L5, and the selection pressures differed between both groups. Regulatory proteins appeared to evolve neutrally in L5 but under purifying selection in L6. Conversely, human T cell epitopes were under purifying selection in L5, but under positive selection in L6. Although only 10% of the T cell epitopes were variable, mutations were mostly lineage-specific. Our findings indicate that Maf L5 and L6 are genomically distinct, possibly reflecting different ecological niches.

genomics↗