Genomic Interactions Between Mycobacterium tuberculosis and Humans.

Mycobacterium tuberculosis is considered by many to be the deadliest microbe, with the estimated annual cases numbering more than 10 million. The bacteria, including Mycobacterium africanum, are classified into nine major lineages and hundreds of sublineages, each with different geographical distributions and levels of virulence. The phylogeographic patterns can be a result of recent and early human migrations as well as coevolution between the bacteria and various human populations, which may explain why many studies on human genetic factors contributing to tuberculosis have not been replicable in different areas. Moreover, several studies have revealed the significance of interactions between human genetic variations and bacterial genotypes in determining the development of tuberculosis, suggesting coadaptation. The increased availability of whole-genome sequence data from both humans and bacteria has enabled a better understanding of these interactions, which can inform the development of vaccines and other control measures.

Effects of two novel denture cleansers on multispecies microbial biofilms, stain removal and the denture surface: an in vitro study.

BACKGROUND: The continuously increasing demand for removable denture appliances and the importance of adequate denture cleaning have led to the development of various denture cleansing products. The aim of this study was to evaluate the efficacy of two novel denture cleansing agents (GE and TM) and three commonly available cleansers (0.5% sodium hypochlorite; NaClO, 0.12% chlorhexidine gluconate; CHX, and Polident®; POL) on multispecies microbial biofilm formation, stain removal and physical properties of dentures. METHODS: The antimicrobial activities of denture cleansing agents were determined against major oral opportunistic pathogens including Streptococcus mutans, Staphylococcus aureus, Escherichia coli and Candida albicans, using time-kill assays. Multispecies microbial biofilms grown on acrylic resins for 72 h were generated to determine the antibiofilm effects of cleansing agents by confocal laser scanning microscopy (CLSM). Evaluations of the tea and coffee stain removal properties and the alterations in the physical properties of dentures were also performed. The toxicity of cleanser residues released from denture acrylics to fibroblast cells was investigated using MTT assay. RESULTS: All denture cleansing agents tested could effectively kill oral bacteria and Candida albicans. Furthermore, after immersion for more than 3 h, the cleansers Polident®, GE and TM could efficiently penetrate and inhibit multispecies denture biofilms with effects similar to 10 min of immersion in 0.5% NaClO. However, immersion in 0.12% CHX for 20 min showed less antibiofilm activity. The NaClO solution had the highest efficacy for removing stains from the artificial teeth. Conversely, the CHX solution enhanced tea and coffee staining, and the teeth immersed in this solution showed clinically unacceptable colour changes (ΔE > 5.5). However, the colour differences of teeth stained and immersed in POL, GE and TM cleansers were in the clinically acceptable range. There was no significant difference among the POL, GE and TM cleansers in terms of stain removal efficacy. The cleansers GE and TM did not alter the surface roughness and colour of the materials, moreover the residues of both cleansers did not exhibit cytotoxicity. CONCLUSION: Two novel denture cleansing agents containing natural products, GE and TM exhibited effective antimicrobial activity, antibiofilm and stain removal capabilities without toxicity or disturbance of the physical properties of acrylics.

Novel vinegar solution for denture-cleansing agent.

PURPOSE: To study the antimicrobial effects of a novel vinegar-based denture cleansing agent on oral Streptococci and Candida species and the inhibitory effects on pre-formed bacterial and Candida biofilms on denture base. METHODS: The microorganisms used in this study were Streptococcus mutans (S. mutans), Streptococcus sobrinus (S. sobrinus), Streptococcus sanguinis (S. sanguinis), Candida albicans (C. albicans), and Candida glabrata (C. glabrata). The antimicrobial activity of novel vinegar solution was evaluated by time kill assay and biofilm grown on denture base. RESULTS: Time kill assay showed that vinegar exhibited the highest antibacterial effect on S. sobrinus, S. sanguinis, and S. mutans after 15 min of treatment. A 99.9% reduction in C. glabrata and C. albicans required more than 4 and 6 h of treatment, respectively. Vinegar significantly inhibited streptococcal biofilm, with an approximately 6 log-reduction at 30 min of treatment. The results demonstrated that viable Candida cells in biofilm reduced in excess of 6-log CFU/mL after 3 h treatment with vinegar. Moreover, the vinegar-based denture cleanser inhibited bacterial and Candida biofilm formation compared to the control group without treatment with statistical significance. CONCLUSION: A novel vinegar-based denture cleansing agent showed moderate antibacterial properties, but required a slightly longer immersion time to attain anticandidal effects compared to Polident and 0.2% CHX.

The effect of Er,Cr:YSGG laser on periodontopathic bacteria elimination: an in vitro study.

In vitro bacterial elimination using the erbium, chromium: yttrium-scandium-gallium-garnet (Er,Cr:YSGG) laser against periodontopathic bacteria was investigated. Bacterial suspensions of Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis were spread on agar plates and the Er,Cr:YSGG laser was applied at 40 mJ pulse energy for durations of 30 s, 60 s, and 90 s. The agar plates were incubated, and growth inhibition zones were assessed. Optimal laser irradiation durations to achieve maximal bacterial elimination were evaluated using laser ablation on the bacterial colonies. The remaining viable bacteria were determined by the colony-forming unit (CFU) counting method. Growth inhibition zones were observed at all irradiation durations for both A. actinomycetemcomitans and P. gingivalis. Mean logarithmic values of CFU/ml after bacterial colony irradiation for 0 s (control), 12 s × 1 lap, 24 s × 1 lap, 48 s × 1 lap, and 24 s × 2 laps were 8.82 ± 0.35, 7.31 ± 0.94, 6.32 ± 0.61, 3.17 ± 2.90, and 0.00, respectively, for A. actinomycetemcomitans and 9.83 ± 0.50, 9.42 ± 0.11, 6.90 ± 1.60, 2.33 ± 3.19, and 0.00 for P. gingivalis. Significant differences were found between the control group and the two irradiated groups 48 s × 1 lap and 24 s × 2 laps (p < 0.05), and also between irradiated groups 12 s × 1 lap and 24 s × 2 laps (p < 0.05). An Er,Cr:YSGG laser with power setting 1.5 W and 30 Hz frequency showed potential for bacterial elimination against A. actinomycetemcomitans and P. gingivalis in vitro. Significant bacterial elimination (> 99.99%) was observed after 48 s of irradiation.

Geraniol and thymoquinone inhibit Candida spp. biofilm formation on acrylic denture resin without affecting surface roughness or color.

PURPOSE: This study was designed to investigate the in vitro effects of geraniol (GE) and thymoquinone (TQ) on Candida biofilms on denture acrylic and any accompanying changes in acrylic surface roughness or color. METHODS: The susceptibility of Candida species to GE and TQ was determined using the broth microdilution method and time-kill assay. A minimum biofilm eradication concentration (MBEC) assay was performed using 7-day Candida biofilms grown on denture acrylic. RESULTS: The minimum inhibitory concentration (MIC) of GE and TQ for Candida spp. was 256 and 32 µg/mL, respectively. The Candida strain complete kill rates for GE and TQ at 5-fold MIC were determined after 1 h of incubation. At 5-fold MIC, GE and TQ inhibited the preformed biofilm activity (MBEC80) of all Candida strains on denture acrylic by more than 80% after treatment for 3 h. At sub-MIC levels, GE and TQ prevented the development of C. albicans and C. tropicalis hyphae. SEM images demonstrated that GE and TQ damaged the fungal cell membrane and induced cell lysis. On the other hand, GE and TQ at 10-fold MIC did not alter the surface roughness or color of the denture acrylic. CONCLUSION: GE and TQ are interesting natural substances that could be developed as promising disinfectants for removable dentures.

Identification and in silico functional prediction of lineage-specific SNPs distributed in DosR-related proteins and resuscitation-promoting factor proteins of Mycobacterium tuberculosis.

One-third of the world population is infected by Mycobacterium tuberculosis, which may persist in the latent or dormant state. Bacteria can shift to dormancy when encountering harsh conditions such as low oxygen, nutrient starvation, high acidity and host immune defenses. Genes related to the dormancy survival regulator (DosR) regulon are responsible for the inhibition of aerobic respiration and replication, which is required to enter dormancy. Conversely, resuscitation-promoting factor (rpf) proteins participate in reactivation from dormancy and the development of active tuberculosis (TB). Many DosR regulon and rpf proteins are immunodominant T cell antigens that are highly expressed in latent TB infection. They could serve as TB vaccine candidates and be used for diagnostic development. We explored the genetic polymorphisms of 50 DosR-related genes and 5 rpf genes among 1,170 previously sequenced clinical M. tuberculosis genomes. Forty-three lineage- or sublineage-specific nonsynonymous single nucleotide polymorphisms (nsSNPs) were identified. Ten nsSNPs were specific to all Mtb isolates belonging to lineage 1 (L1). Two common sublineages, the Beijing family (L2.2) and EAI2 (L1.2.1), differed at as many as 26 lineage- or sublineage-specific SNPs. DosR regulon genes related to membrane proteins and the rpf family possessed mean dN/dS ratios greater than one, suggesting that they are under positive selection. Although the T cell epitope regions of DosR-related and rpf antigens were quite conserved, we found that the epitopes in L1 had higher rates of genetic polymorphisms than the other lineages. Some mutations in immunogenic epitopes of the antigens were specific to particular M. tuberculosis lineages. Therefore, the genetic diversity of the DosR regulon and rpf proteins might impact the adaptation of M. tuberculosis to the dormant state and the immunogenicity of latency antigens, which warrants further investigation.

Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis.

Homoplastic mutations are mutations independently occurring in different clades of an organism. The homoplastic changes may be a result of convergence evolution due to selective pressures. Reports on the analysis of homoplastic mutations in Mycobacterium tuberculosis have been limited. Here we characterized the distribution of homoplastic single nucleotide polymorphisms (SNPs) among genomes of 1,170 clinical M. tuberculosis isolates. They were present in all functional categories of genes, with pe/ppe gene family having the highest ratio of homoplastic SNPs compared to the total SNPs identified in the same functional category. Among the pe/ppe genes, the homoplastic SNPs were common in a relatively small number of homologous genes, including ppe18, the protein of which is a component of a promising candidate vaccine, M72/AS01E. The homoplastic SNPs in ppe18 were particularly common among M. tuberculosis Lineage 1 isolates, suggesting the need for caution in extrapolating the results of the vaccine trial to the population where L1 is endemic in Asia. As expected, homoplastic SNPs strongly associated with drug resistance. Most of these mutations are already well known. However, a number of novel mutations associated with streptomycin resistance were identified, which warrants further investigation. A SNP in the intergenic region upstream of Rv0079 (DATIN) was experimentally shown to increase transcriptional activity of the downstream gene, suggesting that intergenic homoplastic SNPs should have effects on the physiology of the bacterial cells. Our study highlights the potential of homoplastic mutations to produce phenotypic changes. Under selective pressure and during interaction with the host, homoplastic mutations may confer advantages to M. tuberculosis and deserve further characterization.

Oral Lactobacilli Related to Caries Status of Children with Primary Dentition.

Oral lactobacilli are members of a group of bacteria implicated in caries progression, although information regarding their transmission, colonization, and caries-associated species is not well established. This study isolated oral lactobacilli from a group of children with primary dentition for determination of Lactobacillus prevalence, detection of Streptococcus mutans, a major pathogen of caries initiation, and dental caries status of the children. Species of Lactobacillus isolates were determined from examination of 16S rDNA sequences. Subsequently, the most prevalent species was evaluated for involvement in caries status, and binding ability to type I collagen of all Lactobacillus isolates was determined in association with caries status. Multilocus sequence typing (MLST) of eleven loci was carried out to study strains of the predominant Lactobacillus sp. The detection of oral lactobacilli together with S. mutans was significantly associated with the highest dental caries indices, but there was no involvement of collagen-binding properties of Lactobacillus isolates in caries status. Lactobacillus fermentum was the most prevalent, and its presence was related to high scores of caries indices. MLST analysis of L. fermentum population could not specify a particular clone associated with caries status, but revealed sharing of identical L. fermentum strains among children in the same classrooms. Taken together, the data contributed useful information on the role of oral lactobacilli, in particular L. fermentum in dental caries.

A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages.

Global Mycobacterium tuberculosis population comprises 7 major lineages. The Beijing strains, particularly the ones classified as Modern groups, have been found worldwide, frequently associated with drug resistance, younger ages, outbreaks and appear to be expanding. Here, we report analysis of whole genome sequences of 1170 M. tuberculosis isolates together with their patient profiles. Our samples belonged to Lineage 1-4 (L1-L4) with those of L1 and L2 being equally dominant. Phylogenetic analysis revealed several new or rare sublineages. Differential associations between sublineages of M. tuberculosis and patient profiles, including ages, ethnicity, HIV (human immunodeficiency virus) infection and drug resistance were demonstrated. The Ancestral Beijing strains and some sublineages of L4 were associated with ethnic minorities while L1 was more common in Thais. L2.2.1.Ancestral 4 surprisingly had a mutation that is typical of the Modern Beijing sublineages and was common in Akha and Lahu tribes who have migrated from Southern China in the last century. This may indicate that the evolutionary transition from the Ancestral to Modern Beijing sublineages might be gradual and occur in Southern China, where the presence of multiple ethnic groups might have allowed for the circulations of various co-evolving sublineages which ultimately lead to the emergence of the Modern Beijing strains.

Missense mutation in CgPDR1 regulator associated with azole-resistant Candida glabrata recovered from Thai oral candidiasis patients.

OBJECTIVES: Non-albicans Candida (NAC) species are increasingly identified as pathogens causing oral candidiasis. Incidence rates for azole resistance among NAC species have been continuously reported. This study aimed to evaluate the azole susceptibility profiles and to characterise the azole resistance mechanisms of oral clinical NAC isolates. METHODS: In vitro susceptibility patterns of 85 NAC species isolates were determined by the broth microdilution method. Azole resistance-related genes (ERG3, ERG11 and PDR1) of Candida glabrata isolates were sequenced to determine the presence of nucleotide substitutions. Expression levels of various resistance-related genes were also evaluated by RT-qPCR in azole-susceptible, susceptible dose-dependent (SDD) and resistant Candida isolates. RESULTS: Two C. glabrata isolates (2.4% of all NAC isolates) were resistant to all three azoles tested (fluconazole, itraconazole and ketoconazole). All clinical isolates of Candida tropicalis and Candida kefyr were susceptible to azoles. Silent mutations were found in the CgERG11 and CgERG3 genes of clinical C. glabrata isolates. Interestingly, two missense mutations in CgPDR1 (N768D and E818K) were identified only in resistant C. glabrata isolates. The presence of a CgPDR1 missense mutation in resistant isolates is associated with overexpression of its own product as well as multidrug transporters including ABC and MFS transporters. CONCLUSION: A gain-of-function (GOF) mutation in CgPDR1 is associated with upregulation of various drug transporters, which appears to serve as a primary mechanism for azole resistance in the detected C. glabrata isolates. Therefore, analysis of GOF mutations in the PDR1 regulator provides a better understanding of the development of antifungal resistance.

Genotyping of Candida albicans and Candida dubliniensis by 25S rDNA analysis shows association with virulence attributes in oral candidiasis.

OBJECTIVES: This study genotyped oral isolates of Candida albicans and C. dubliniensis by analyzing 25S rDNA transposable intron and evaluated their virulence attributes in oral candidiasis. DESIGN: C. albicans and C. dubliniensis were isolated from oral cavity of normal carriers (n = 100) and oral candidiasis patients (n = 100), genotyped by PCR, and virulence properties, namely, secreted phospholipase and proteinase activities (using an agar plate method) and binding to buccal epithelial cells, were determined. In addition, antifungal sensitivity was assayed for all Candida isolates. RESULTS: C. albicans genotypes A, B, C and D (C. dubliniensis) were identified. Genotype B was the most prevalent in both healthy and candidiasis groups and had highest buccal epithelial cell binding ability but lowest secreted phospholipase activity. Genotype C was the third most prevalent, with higher frequency in patients than normal carriers. Genotype A, the second most prevalent, was equally found in both groups. There were no significant differences in secreted proteinase activity among the three C. albicans genotypes. C. dubliniensis, the least prevalent, was more frequent in healthy carriers and demonstrated minimal levels of the virulence properties. When all Candida isolates were compared based on groups of subjects, only secreted phospholipase activity was significantly higher in isolates from candidiasis patients. All Candida isolates were susceptible to clotrimazole, fluconazole, miconazole and nystatin. CONCLUSIONS: Genotyping based on the 25S rDNA transposable intron region provided a simple method allowing studies of the pathogenicity of each genotype.

Cariogenic properties of Streptococcus mutans clinical isolates with sortase defects.

OBJECTIVE: In Streptococcus mutans, a Gram-positive pathogen of dental caries, several surface proteins are anchored by the activity of sortase enzyme. Although various reports have shown that constructed S. mutans mutants deficient of sortase as well as laboratory reference strains with a sortase gene mutation have low cariogenic potential, no known studies have investigated clinical isolates with sortase defects. Here, we examined the cariogenic properties of S. mutans clinical isolates with sortase defects as well as caries status in humans harboring such defective isolates. DESIGN: Sortase-defective clinical isolates were evaluated for biofilm formation, sucrose-dependent adhesion, stress-induced dextran-dependent aggregation, acid production, and acid tolerance. Additionally, caries indices of subjects possessing such defective isolates were determined. RESULTS: Our in vitro results indicated that biofilm with a lower quantity was formed by sortase-defective as compared to non-defective isolates. Moreover, impairments of sucrose-dependent adhesion and stress-induced dextran-dependent aggregation were found among the isolates with defects, whereas no alterations were seen in regard to acid production or tolerance. Furthermore, glucan-binding protein C, a surface protein anchored by sortase activity, was predominantly detected in culture supernatants of all sortase-defective S. mutans isolates. Although the sortase-defective isolates showed lower cariogenic potential because of a reduction in some cariogenic properties, deft/DMFT indices revealed that all subjects harboring those isolates had caries experience. CONCLUSIONS: Our findings suggest the impairment of cariogenic properties in S. mutans clinical isolates with sortase defects, though the detection of these defective isolates seemed not to imply low caries risk in the subjects harboring them.

Cell-Free DNA Profile in Peri-Implant Skin Exudate of Craniofacial Implants with Various Degrees of Inflammation: A Pilot Study.

PURPOSE: To profile human ß-globin gene fragment lengths from cell-free DNA in peri-implant skin exudate of craniofacial implants with various degrees of soft tissue inflammation. MATERIALS AND METHODS: Fifteen participants (30 implants) were recruited for this study. All participants were recalled for three consecutive visits at days 0, 14, and 28. During each visit, the soft tissue condition at the skin-abutment interface of each craniofacial implant was graded by Holgers score, and the implant stability quotient (ISQ) values of the implants were also measured. Peri-implant skin exudate specimens were collected and centrifuged to obtain cell-free DNA. Conventional polymerase chain reaction was used to assess DNA fragment lengths by amplifying five polymerase chain reaction amplicon sizes from 110-base pairs (bp) to 2-kilobase pairs (kbp) of human ß-globin gene. The longest polymerase chain reaction amplicon size found in each specimen was then recorded. RESULTS: No significant differences in the ISQ values of the implants (P > .05) were noted during the study period. In each recall visit, a correlation was observed between Holgers score and polymerase chain reaction amplicon sizes (P < .001). A gradual decrease in both parameters was also noted following the treatment protocol (P < .05). From the 90 exudate specimens obtained from all the observation visits, 1-kbp amplicon sizes were usually found in the group with Holgers score 1 (47 of 52 specimens); 2-kbp amplicon sizes were often found in the group with Holgers score 2 (22 of 32 specimens) and predominantly found in the group with Holgers score 3 (5 of 6 specimens). CONCLUSION: The 1-kbp amplicon sizes can serve as a marker for mild clinical inflammation of peri-implant skin. Similarly, 2-kbp amplicon sizes may be used as a prognostic marker for denoting greater cell destruction and inflammation, which indicate a greater risk of severe inflammation. However, further studies are required to support these findings.

Biomarkers for Refractory Lupus Nephritis: A Microarray Study of Kidney Tissue.

The prognosis of severe lupus nephritis (LN) is very different among individual patients. None of the current biomarkers can be used to predict the development of refractory LN. Because kidney histology is the gold standard for diagnosing LN, the authors hypothesize that molecular signatures detected in kidney biopsy tissue may have predictive value in determining the therapeutic response. Sixty-seven patients with biopsy-proven severely active LN by International Society of Nephrology/Renal Pathology Society (ISN/RPS) classification III/IV were recruited. Twenty-three kidney tissue samples were used for RNA microarray analysis, while the remaining 44 samples were used for validation by real-time polymerase chain reaction (PCR) gene expression analysis. From hundreds of differential gene expressions in refractory LN, 12 candidates were selected for validation based on gene expression levels as well as relevant functions. The candidate biomarkers were members of the innate immune response molecules, adhesion molecules, calcium-binding receptors, and paracellular tight junction proteins. S100A8, ANXA13, CLDN19 and FAM46B were identified as the best kidney biomarkers for refractory LN, and COL8A1 was identified as the best marker for early loss of kidney function. These new molecular markers can be used to predict refractory LN and may eventually lead to novel molecular targets for therapy.

Distribution of Candida albicans and non-albicans Candida species in oral candidiasis patients: Correlation between cell surface hydrophobicity and biofilm forming activities.

OBJECTIVES: The purposes of this investigation were to study the prevalence of Candida albicans and non-albicans Candida (NAC) species from oral candidiasis patients and evaluate the cell surface hydrophobicity (CSH) and biofilm forming capacity of the clinical isolates Candida species from oral cavity. DESIGN: This study identified a total of 250 Candida strains isolated from 207 oral candidiasis patients with PCR-RFLP technique. CSH value, total biomass of biofilm and biofilm forming ability of 117 oral Candida isolates were evaluated. RESULTS: C. albicans (61.6%) was still the predominant species in oral candidiasis patients with and without denture wearer, respectively, followed by C. glabrata (15.2%), C. tropicalis (10.4%), C. parapsilosis (3.2%), C. kefyr (3.6%), C. dubliniensis (2%), C. lusitaniae (2%), C. krusei (1.6%), and C. guilliermondii (0.4%). The proportion of mixed colonization with more than one Candida species was 18% from total cases. The relative CSH value and biofilm biomass of NAC species were greater than C. albicans (p<0.001). Ninety-two percent of oral isolates NAC species had biofilm forming ability, whereas 78% of C. albicans were biofilm formers. Furthermore, the significant difference of relative CSH values between biofilm formers and non-biofilm formers was observed in the NAC species (p<0.005), whereas the difference was not statistically significant in C. albicans. CONCLUSION: The frequency of the NAC species colonization in oral cavity was gradually increasing. The possible contributing factors might be high cell surface hydrophobicity and biofilm forming ability. The relative CSH value could be a putative factor for determining biofilm formation ability of the non-albicans Candida species.

APRIL, a proliferation-inducing ligand, as a potential marker of lupus nephritis.

INTRODUCTION: BLyS and APRIL are cytokines from the tumor necrosis factor family which play an important role in systemic lupus erythematosus (SLE). Previous works suggested an association between both molecules and SLE disease activity although their correlation with lupus nephritis is not known. We therefore assessed serum BLyS and APRIL in active lupus nephritis patients. METHODS: Serum samples from active lupus nephritis and at 6 months post-treatment were obtained. Serum levels of BLyS and APRIL (n = 47) as well as renal mRNA expression were measured. Serum levels of both molecules and clinical data (n = 27) were available at 6 months follow-up. All biopsy-proven lupus nephritis patients were treated with similar immunosuppressive drugs. RESULTS: Serum levels of APRIL were associated with proteinuria (Rs = 0.44, P value < 0.01) and degree of histological activity (Rs = 0.34; P value < 0.05) whereas BLyS levels were associated with complement levels (Rs = 0.46; P value < 0.01) and dosage of immunosuppressant. Interestingly, serum APRIL as well as its intrarenal mRNA levels were associated with resistance to treatment. From the receiver operating characteristic (ROC) analysis, high levels (> 4 ng/mL) of serum APRIL predicted treatment failure with a positive predictive value of 93 percent. CONCLUSION: APRIL could be a potential biomarker for predicting difficult-to-treat cases of lupus nephritis.