Search Results (24)

Background: Aggregatibacter actinomycetemcomitans JP2 genotype is a virulent pathogen linked to severe periodontitis and systemic diseases. Honey and royal jelly (RJ) have demonstrated bioactive properties against this microorganism. This study aims to assess the bioactive properties of honeys and RJ against this key periodontal pathogen and to preliminarily identify key compounds with antibacterial potential. Methods: The antibacterial activity of honeys and commercial products (manuka, L-Mesitran^® as a medical-grade honey-based formulation (MGHF), and Honix^® RJ) against A. actinomycetemcomitans JP2 was evaluated using the agar well diffusion method and microdilution assays. Extensive physicochemical characterization (e.g., hydrogen peroxide level, total phenolic content, and total flavonoid content) was conducted to correlate the bioactive compounds with the antimicrobial activity. Results: All tested samples exhibited varying antibacterial potency, with inhibition zones ranging from 21 to 37 mm. The MICs ranged from 40.7 to 104.3 mg/mL. MGHF, RJ, and multifloral honeys showed the lowest MICs. The pH of six out of eight samples could not induce enamel decalcification while the pH of three samples may not influence cementum demineralization. Vitamin C, zinc, magnesium, and potassium were present in measurable quantities, and were not associated with significant antibacterial activity. MGHF showed the highest hydrogen peroxide activity and TFC values. TFC and H₂O₂ content were statistically correlated with lower MIC values. Conclusions: Honey and RJ showed antibacterial activity against A. actinomycetemcomitans JP2, partly attributed to their content of hydrogen peroxide and flavonoids. Clinical trials are needed to confirm the potential role of honey, RJ, and their bioactive compounds in managing periodontitis. Full article

Phlegmariurus, a diverse genus within the Lycopodiaceae family, has wide diversity in tropical regions, including Thailand. Accurate species delimitation in the tropical clubmoss genus Phlegmariurus is challenged by high morphological plasticity and genetic complexity. This study applied an integrative multilocus approach combining morphometric analysis of 27 complete specimens, 35 Phlegmariurus and one Lycopodiella accessions for AFLP genotyping (926 loci; PIC 0.32), SSR profiling (44 loci; PIC 0.57; expected heterozygosity 0.35), and chloroplast barcoding using rbcL (1308 bp; bootstrap 89–99%) and the psbA-trnH intergenic spacer (308 bp; bootstrap ≥ 94%). A total of 13 were identified as belonging to seven known species, including P. nummulariifolius (NST01, NST15, NST36), P. goebelii (JP04), P. phlegmaria (NST13), P. verticillatus (PHI16), P. squarrosus (NST21, NST22, MY31), P. tetrastichus (NST30), and P. carinatus (MY32, MY33, NST34). Morphological clustering and molecular markers consistently distinguished Phlegmariurus accessions from the Lycopodiella outgroup. Additionally, 19 previously unclassified Phlegmariurus accessions were successfully identified as belonging to the species P. nummulariifolius (NST23), P. goebelii (NST03, JP05, STN12, PNA14, SKA25, CPN26, KRB27, PNA28), P. phlegmaria (NWT07, STN08, NST09, NST10, PHI29), P. squarrosus (NST17), and P. carinatus (PNA06, STN18, CPN19, JP24). Moreover, this study identified three novel lineages (NST02, STN11, NST20) with strong support across datasets. The combination of broad genomic coverage (AFLP), fine-scale allelic resolution (SSR), deep-branch backbone (rbcL), and terminal-branch discrimination (psbA-trnH) yields a robust framework for species identification. These results define clear operational units for conservation prioritization and establish a foundation for marker-assisted development of ornamental Phlegmariurus cultivars. Full article

Aim: The main purpose of the present study was to investigate the carrier rate of Aggregatibacter actinomycetemcomitans and its JP2 genotype in a cohort of 200 Western Australians diagnosed with periodontitis. Materials and Methods: In this descriptive cross-sectional study, 220 consecutive patients with periodontitis, aged 18 years and older, were recruited to a specialist periodontal practice in Perth City. Every patient included in this study contributed three different intra-oral samples. Periodontal, radiographical, and microbiological assessments were performed. The samples were analysed using a polymerase chain reaction for the detection of Aggregatibacter actinomycetemcomitans and its JP2 genotype using the primers and conditions described previously. A Chi-square test and logistic regression analysis were performed to evaluate the results. Results: The prevalence of Aggregatibacter actinomycetemcomitans was 28.18%. The carrier rates of A. actinomycetemcomitans in the unstimulated saliva, cheek swabs, and pooled subgingival plaque samples were 21.80%, 19.50%, and 17.70%, respectively. There was a significant correlation between the severe form of periodontitis (stage IV, grade C) and younger age (p = 0.004), positive family history of periodontitis (p < 0.001), oral hygiene method (p < 0.001), and irregular dental visit attendance (p < 0.001). The binary logistic regression analysis revealed that having severe periodontitis risk increased almost three times in those who were young (OR: 2.812) and came from a family with a history of periodontal disease (OR: 3.194). However, the risk of severe periodontitis was five times higher in those patients with tooth loss due to periodontal disease (OR: 5.071). The highly leukotoxic JP2 genotype of Aggregatibacter actinomycetemcomitans was not detected. Conclusions: This study of a Western Australian cohort confirmed the low presence of Aggregatibacter actinomycetemcomitans and the complete absence of its JP2 genotype. Young age, family history of periodontal disease, lack of flossing, irregular dental visits, and tooth loss due to periodontitis were identified as potential risk factors for periodontitis stage IV, grade C in this cohort. Full article

Chronic Hepatitis B Virus (HBV) infection remains a significant public health concern, particularly in Africa, where the burden is substantial. HBV is an enveloped virus, classified into ten phylogenetically distinct genotypes (A–J). Tests to determine HBV genotypes are based on full-genome sequencing or reverse hybridization. In practice, both approaches have limitations. Whereas diagnostic sequencing, generally using the Sanger approach, tends to focus only on the S-gene and yields little or no information on intra-patient HBV genetic diversity, reverse hybridization detects only known genotype-specific mutations. To resolve these limitations, we developed an Oxford Nanopore Technology (ONT)-based HBV diagnostic sequencing protocol suitable for clinical virology that yields both complete genome sequences and extensive intra-patient HBV diversity data. Specifically, the protocol involves tiling-based PCR amplification of HBV sequences, library preparation using the ONT Rapid Barcoding Kit (Oxford nanopore Technologies, Oxford, OX4 4DQ, UK), ONT GridION sequencing, genotyping using genome detective software v1.132/1.133, a recombination analysis using jpHMM (26 October 2011 version) and RDP5.61 software, and drug resistance profiling using Geno2pheno v2.0 software. We prove the utility of our protocol by efficiently generating and characterizing high-quality near full-length HBV genomes from 148 residual diagnostic samples from HBV-infected patients in the Western Cape province of South Africa, providing valuable insights into the genetic diversity and epidemiology of HBV in this region of the world. Full article

Adolescent carriers of the Aggregatibacter actinomycetemcomitans JP2 genotype have an increased risk of developing periodontitis, due to the bacterium’s high leukotoxin (LtxA) production. LtxA contributes to marginal bone loss by killing immunity cells, thus activating the proinflammatory interleukin-1β (IL-1β), which, in turn, activates the osteoclasts. A possible strategy to prevent periodontitis might be to neutralize LtxA in JP2-infected individuals. The aim of this study was to investigate whether extracts from Matcha or Guava leaves can prolong the viability of macrophages in cell cultures by neutralizing the highly leukotoxic JP2 genotype bacteria. The A. actinomycetemcomitans JP2 genotype was pretreated with extracts from either Matcha or Guava leaves. Later, the extracts were rinsed off, before JP2 bacteria were exposed to macrophage cell cultures. The experiment was repeated, where JP2 bacteria were persistently treated with the extracts instead, i.e., the extracts were not rinsed off. The macrophage viability after bacterial exposure was analyzed and compared with that of macrophages exposed to untreated JP2 bacteria. IL-1β secretion in the cell culture medium was quantified in all group samples. Pretreatment of the A. actinomycetemcomitans JP2 genotype with Matcha or Guava leaf extracts moderately neutralized LtxA activity, which resulted in prolonged macrophage viability and decreased IL-1β secretion. These effects of prolonged macrophage viability were enhanced when extracts were persistently present during the exposure period. The results indicate that Matcha and Guava leaf extracts have effects on the virulence of the A. actinomycetemcomitans JP2 genotype that may be useful in future treatment strategies to prevent periodontitis in JP2 bacterium carriers. Full article

Aggressive forms of periodontitis, especially in young patients, are often associated with an increased proportion of the Gram-negative bacterium Aggregatibacter actinomycetemcomitans of the microbiota of the affected periodontal sites. One of the virulence factors of A. actinomycetemcomitans is a leukotoxin (LtxA) that induces a pro-inflammatory cell death process in leukocytes. A. actinomycetemcomitans exhibits a large genetic diversity and different genotypes vary in LtxA production capacity. The genotype JP2 is a heavy LtxA producer due to a 530-base pair deletion in the promoter for the toxin genes, and this trait has been associated with an increased pathogenic potential. The present study focused on the production and release of LtxA by different A. actinomycetemcomitans genotypes and serotypes under various growth conditions. Four different strains of this bacterium were cultured in two different culture broths, and the amount of LtxA bound to the bacterial surface or released into the broths was determined. The cultures were examined during the logarithmic and the early stationary phases of growth. The JP2 genotype exhibited the highest LtxA production among the strains tested, and production was not affected by the growth phase. The opposite was observed with the other strains. The composition of the culture broth had no effect on the growth pattern of the tested strains. However, the abundant release of LtxA from the bacterial surface into the culture broth was found in the presence of horse serum. Besides confirming the enhanced leucotoxicity of the JP2 genotype, the study provides new data on LtxA production in the logarithmic and stationary phases of growth and the effect of media composition on the release of the toxin from the bacterial membrane. Full article

The aims of the present study were to document the presence of Aggregatibacter actinomyctemcomitans and the emerging oral pathogen Filifactor alocis, as well as to identify genotypes of these bacterial species with enhanced virulence. In addition, these data were analyzed in relation to periodontal pocket depth (PPD) and the progression of PPD from the sampled periodontal sites during a two-year period. Subgingival plaque samples were collected from 172 periodontal pockets of 68 Ghanaian adolescents. PPD at sampling varied from 3–14 mm and the progression from baseline, i.e., two years earlier up to 8 mm. The levels of A. actinomycetemcomitans and F. alocis were determined with quantitative PCR. The highly leukotoxic JP2-genotype of A. actinomycetemcomitans and the ftxA a gene of F. alocis, encoding a putative Repeats-in-Toxin (RTX) protein, were detected with conventional PCR. The prevalence of A. actinomycetemcomitans was 57%, and 14% of the samples contained the JP2 genotype. F. alocis was detected in 92% of the samples and the ftxA gene in 52%. The levels of these bacterial species were significantly associated with enhanced PPD and progression, with a more pronounced impact in sites positive for the JP2 genotype or the ftxA gene. Taken together, the results indicate that the presence of both A. actinomycetemcomitans and F. alocis with their RTX proteins are linked to increased PPD and progression of disease. Full article

The Montenegrin sheep population mostly consists of local breeds and their crossbreeds that are very valuable from their genome preservation point of view. The aim of this study was the investigation of the genetic diversity of seven Montenegrin sheep breeds (Jezeropivska—JP, Sora—SOR, Zetska zuja—ZZ, Bardoka—BAR, Sjenička—SJ, Ljaba—Lj, and Piperska zuja—PIP) using 18 microsatellite sets of markers. The genotyping was done for 291 samples from seven populations using the multiplex amplification of sequences with polymerase chain reaction (PCR). The parameters of genetic diversity were estimated using several software tools. In total, 243 alleles were found, with a range of 6 to 25 by locus. The mean observed heterozygosity (Ho), polymorphism information content (PIC), and Fis values (fixation index) per marker were 0.728, 0.781, and −0.007, respectively. The mean number of alleles per breed varied from 4.889 in ZZ to 10.056 in JP. The highest Ho was estimated for JP (0.763) and the lowest for ZZ (0.640). The genetic structure showed close relations between SOR and JP, and both of them with SJ, while ZZ, LJ, and PIP were more distanced. This study provides useful indicators for the development of further in-depth studies and the creation of appropriate conservation programs. Full article

The JP2 genotype of Aggregatibacter actinomycetemcomitans serotype b is associated with aggressive forms of periodontitis and was initially identified as affecting adolescents in North and West Africa. The dissemination of this genotype follows the migration routes and can today be detected in samples from periodontitis patients in a high number of countries. In the present study, we aim to describe findings of the JP2 genotype A. actinomycetemcomits in a clinical laboratory at the Dental School, Odontology, Umeå University, Sweden. The findings of JP2 carriers are documented during a 21-year period, and the age and geographic origin of the sampled individuals are described. In addition, the collected JP2 isolates were separated into North or West African origin by analyses of the presence of a point mutation in the hbpA2 pseudogene of the bacterium. In a total of 2296 sampled individuals during this period in this Swedish population of periodontitis patients, 32 JP2 carriers were detected by cultivation and PCR. The geographic background of these individuals was diverse, including sixteen with African origin, ten with a Swedish origin and six additional ones with a non-African origin. The JP2 genotypes of A. actinomycetemcomitans were mainly isolated from young individuals (<35 years of age), and seven out of the 32 isolates were of a West African origin based on the sequence of hbpA2. We conclude that the JP2 genotype of A. actinomycetemcomitans can be detected world-wide in subgingival plaque samples from adolescents affected by periodontitis. Full article

In an effort to evaluate the accuracy of HIV-1 phylogenies based on genomes of increasing length, we developed a comprehensive near-full-length HIV-1 genome RT–PCR assay and performed a comparative evaluation via phylogenetic analyses. To this end, we conducted comparative analyses of HIV-1 phylogenies derived based on HIV-1 PR/RT (2253–3359 in the HXB2 genome) and pol region (2253–5250 in the HXB2 genome) sequences isolated from 134 HIV-1-infected patients in Cyprus (2017–2019). The HIV-1 genotypic subtypes determined using six subtyping tools (REGA 3.0, COMET 2.3, jpHMM, SCUEAL, Stanford, and Geno2pheno) were compared to investigate the discrepancies generated among different tools. To evaluate the accuracy of defined HIV-1 phylogenies, the samples exhibiting at least one discrepant subtyping result among different subtyping tools in both PR/RT and pol regions or only in the pol region (n = 38) were selected for near-full-length HIV-1 genome (790–8795 in HXB2 genome) sequencing using a newly developed RT–PCR/sequencing assay. The obtained sequences were employed for HIV-1 genotypic subtype determination and subjected to comparative phylogenetic-based analyses. It was observed that 39.6% of the 134 samples presented discrepancies in the PR/RT region, while 28.4% presented discrepancies in the pol region. REGA 3.0 produced the fewest discrepancies collectively in both regions and was selected for subsequent subtyping and comparative phylogenetic analyses of near-full-length HIV-1 genome sequences. The analyses of near-full-length HIV-1 genome sequences identified 68.4% of the 38 ‘discrepant samples’ (n = 26) as belonging to uncharacterized recombinant HIV-1 strains, while 21.1% were circulating recombinant forms (CRFs) (n = 8) and 10.5% belonged to pure group M subtypes (n = 4). The findings demonstrated a significant reduction of 11.2% in discrepancies when pol region sequences were used compared to PR/RT region sequences, indicating that increased nucleotide sequence lengths are directly correlated with more consistent subtype classification. The results also revealed that if the discrepancy in pol region subtyping results persists, then there is a high likelihood (89.5%) that the query sequence is a recombinant HIV-1 strain, 68.4% of which belong to uncharacterized recombinant HIV-1 strains. The results of this study showed that REGA 3.0 presented the best performance in subtyping recombinant HIV-1 strains, while Stanford performed better in defining phylogenies of pure group M subtypes. The study highlights that, especially in populations with polyphyletic HIV-1 epidemics resulting in a high prevalence of recombinant HIV-1 strains, neither PR/RT nor pol region sequences are reliable for the determination of HIV-1 genotypic subtypes in samples showing discrepancies among different subtyping tools, and only near-full-length or full-length HIV-1 genome sequences are sufficiently accurate. Full article

Aggregatibacter actinomycetemcomitans is strongly associated with severe periodontitis, possibly due to its production of a potent leukotoxin. A genetic variant, the JP2 genotype, was found to produce more leukotoxin than the wild type because of a mutation in the leukotoxin gene, and this genotype is frequently found in African populations. The aim of this study was to investigate whether this JP2 genotype can be found in a randomly selected group of inhabitants of Sal, Cape Verde. Twenty-nine adults between 20 and 59 years of age (58.6% female) participated, and information on their oral health and living standards was collected. An oral examination was performed for each participant, including DMF-T and CPI scores. Plaque and saliva samples were collected and transported to Europe, where DNA was isolated, and the concentration of A. actinomycetemcomitans and its JP2 genotype was determined using dedicated PCR analyses. All 29 plaque and 31% of the saliva samples harboured A. actinomycetemcomitans, and two participants were positive for the JP2 genotype. The presence of this JP2 genotype was not associated with either CPI or DMF-T. This pilot study is the first to describe the presence of the A. actinomycetemcomitans JP2 genotype in a Cape Verdean population living in the Cape Verde Islands, and the findings warrant further research. Full article

The complete nucleotide sequence of the S1 glycoprotein gene of the Japanese infectious bronchitis virus (IBV) strains was determined and genetically analyzed. A total of 61 Japanese IBV strains were classified into seven genotypes, namely GI-1, 3, 7, 13, 18, 19, and GVI-1 using the classification scheme that was proposed by Valastro et al, with three exceptions. These genotypes practically corresponded to those defined in Japan, namely Mass, Gray, JP-II, 4/91, JP-I, JP-III, and JP-IV, which have been identified through their partial nucleotide sequences containing hypervariable regions 1 and 2. In addition, three exceptive strains were considered to be derived from recombination within the S1 gene of IBV strains G1-13 and GI-19. By analyzing the amino acid polymorphism of the S1 glycoprotein among Japanese genotypes, a diversity was observed based on the genotype-specific amino acid residue, the proteolytic cleavage motif at the S1/S2 cleavage site, and the position of the potential N-glycosylation sites. Full article

The Aggregatibacter actinomycetemcomitans JP2 genotype is associated with high leukotoxin production and severe (aggressive) periodontitis. The aim of this study was to compare the antimicrobial susceptibility of JP2 and non-JP2 genotype strains. Minimal inhibitory concentrations (MICs) of 11 antimicrobials were determined for 160 A. actinomycetemcomitans of serotype a, b, or c, mostly isolated in Sweden or Ghana. MIC distributions for benzylpenicillin and fusidic acid revealed a more susceptible subpopulation for 38 serotype b strains, including the 32 of the JP2 genotype, with a benzylpenicillin MIC range of 0.125–0.5 mg/L. In contrast, benzylpenicillin MIC ≤ 16 mg/L was the estimated 99.5% epidemiological cutoff (ECOFF) of all strains. Beta-lactamase production was not detected. The fusidic acid MIC distribution of 11 strains of Aggregatibacter aphrophilus agreed with that found in non-JP2 strains. Cefotaxime, meropenem, levofloxacin, and trimethoprim–sulfamethoxazole MICs were all ≤0.25 mg/L, while MIC₉₀ values for amoxicillin, azithromycin and tetracycline were 1 mg/L. Metronidazole MICs varied between 0.5 and >256 mg/L. The discrepant findings indicate that A. actinomycetemcomitans may be divided into two separate wild types, with a suggested intrinsic reduced susceptibility for benzylpenicillin in the majority of non-JP2 genotype strains. Possible implications for the treatment of A. actinomycetemcomitans infections are discussed. Full article

Background: A virulent genotype (JP2) of the periodonto-pathogen, Aggregatibacter actinomycetemcomitans (Aa), is widespread in North and West Africa, while its presence in East Africa has not been thoroughly investigated. This JP2 genotype is associated with periodontitis in adolescents and has a high leukotoxicity. The aim of the study was to examine the prevalence of Aa and its JP2 genotype, the prevalence of the oral, commensal Aggregatibacter aphrophilus in a Maasai adolescent population, and the effect of herbal plants for inhibition of leukotoxicity. Methods: A total of 284 adolescents from Maasai Mara, Kenya, underwent an oral examination and microbial sampling. The presence of Aa and A. aphrophilus was analyzed by quantitative PCR and cultivation (the 58 samples collected at the last day of field study). The collected Aa strains were characterized and leukotoxin promoter typed. Additionally, herbal plants commonly used for oral hygiene were assessed for the inhibition of leukotoxicity. Results and Conclusions: The prevalence of Aa in stimulated whole saliva was high (71.8%), with the JP2 genotype detected in one individual, and A. aphrophilus in 99% of the sampled individuals. The commonly used herbal plant, Warburgia ugandensis, inactivated Aa leukotoxicity. The Aa virulence might be reduced through use of W. ugandensis and the high levels of A. aphrophilus. Full article

Sesame is sensitive to waterlogging, and its growth is devastatingly impacted under excess moisture conditions. Thus, waterlogging tolerance is crucial to alleviate yield constraints, particularly under expected climate change. In this study, 119 diverse sesame genotypes were screened for their tolerance to 12, 24, 48, and 72 h of waterlogging relative to non-waterlogged conditions. All plants died under 72 h of waterlogging, while 13.45%, 31.93%, and 45.38% of genotypes survived at 48, 24, and 12 h, respectively. Based on the seedling parameters and waterlogging tolerance coefficients, genotypes BD-7008 and BD-6985 exhibited the highest tolerance to waterlogging, while BD-6996 and JP-01811 were the most sensitive ones. The responses of these four genotypes to waterlogged conditions were assessed at different plant growth stages—30, 40, and 50 days after sowing (DAS)—versus normal conditions. Waterlogging, particularly when it occurred within 30 DAS, destructively affected the physiological and morphological characteristics, which was reflected in the growth and yield attributes. Genotype BD-7008, followed by BD-6985, exhibited the highest chlorophyll and proline contents as well as enzymatic antioxidant activities, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). These biochemical and physiological adjustments ameliorated the adverse effects of waterlogging, resulting in higher yields for both genotypes. Conversely, JP-01811 presented the lowest chlorophyll and proline contents as well as enzymatic antioxidant activities, resulting in the poorest growth and seed yield. Full article