Kibdelosporangium persicum sp. nov., a new member of the Actinomycetes from a hot desert in Iran.

Isolate 4NS15T was isolated from a neglected arid habitat in Kerman, Iran. The strain showed 16S rRNA gene sequence similarity values of 98.9 % to the type strains of Kibdelosporangium aridum subsp. aridum, Kibdelosporangium phytohabitans and Kibdelosporangium philippinense and 98.6 % to the type strain K. aridum subsp. largum, respectively. Genome-based phylogenetic analysis revealed that isolate 4NS15T is closely related to Kibdelosporangium aridum subsp. aridum DSM 43828T. The digital DNA-DNA hybridization value between the genome sequences of 4NS15T and strain DSM 43828T is 29.8 %. Strain 4NS15T produces long chains of spores without a sporangium-like structure which can be distinguished from other Kibdelosporangium species. Isolate 4NS15T has a genome size of 10.35 Mbp with a G+C content of 68.1 mol%. Whole-cell hydrolysates of isolate 4NS15T are rich in meso-diaminopimelic acid and cell-wall sugars such as arabinose, galactose, glucose and ribose. Major fatty acids (>10 %) are C16 : 0, iso-C16 : 0 and iso-C15 : 0. The phospholipid profile contains diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylhydroxyethanolamine, aminolipid and glycoaminolipid. The predominant menaquinone is MK-9(H4). Based on its phenotypic and genotypic characteristics, isolate 4NS15T (NCCB 100701=CIP 111705=DSM 110728) merits recognition as representing a novel species of the genus Kibdelosporangium, for which the name Kibdelosporangium persicum sp. nov. is proposed.

Pulmonary actinomycosis diagnosed by radial endobronchial ultrasound coupled with metagenomic next-generation sequencing: A case report and brief literature review.

Pulmonary actinomycosis (PA) is an uncommon pulmonary infectious disease that often is misdiagnosed. Metagenomic next-generation sequencing (mNGS) is a highly sensitive and culture-independent new molecular technology for precise infectious disease diagnosis. Here we report a PA case diagnosed by the combination of a radial endobronchial-ultrasonography guide sheath (R-EBUS-GS) and mNGS, along with a brief review of the literature.

Case Report: Cervicovaginal Co-Colonization with Entamoeba gingivalis and Entamoeba polecki in Association with an Intrauterine Device.

Amoebic trophozoites were identified in the cervicovaginal smear of a U.S. patient without travel history at the time of intrauterine device (IUD) removal. Subsequent morphologic analysis and DNA sequencing identified a mixed cervicovaginal colonization of the female genital tract with both Entamoeba gingivalis and Entamoeba polecki in association with Actinomyces species bacteria. This highlights to the potential for colonization of the genital tract with E. gingivalis, particularly in association with IUD placement, and represents the first report of E. polecki in this context.

Detection of Actinomyces spp. in cervical exudates from women with cervical intraepithelial neoplasia or cervical cancer.

PURPOSE: Under certain circumstances, Actinomyces behaves as an opportunistic microorganism and can cause actinomycosis, a chronic and inflammatory granulomatous infection. The purpose of this project was to detect the presence of Actinomyces in cervical exudates from women with cervical intraepithelial neoplasia (CIN) and women with cervical cancer. METHODOLOGY: Cervical samples from 92 women were divided into three groups: CIN, cervical cancer and healthy women. Metagenomic DNA extraction was performed following the Qiagen QIAamp Mini Kit protocol. A specific fragment (675 bp) was amplified by PCR in order to detect the presence of Actinomycetales. Samples in which Actinomycetales was detected were subjected to separate amplification reactions with primer pairs for A. israelii, A. viscosus, A. meyeri and A. odontolyticus. Amplified products were observed by 2 % agarose gel electrophoresis. RESULTS: Actinomyces were found in 10 % of women with CIN, 36.6 % of women with cervical cancer and 9 % of healthy women. The species identified in this study were A. meyeri in 14/92 samples (15.2 %), A. viscosus in 10/92 samples (10.8 %), A. odontolyticus in 4/92 samples (4.3 %) and A. israelii in 6/92 samples (6.5 %). CONCLUSION: Patients with cervical cancer had a higher prevalence of the presence of Actinomyces compared to the CIN and control groups. This is the first study in which a deliberate search of this genus has been performed in women with cervical pathologies. The use of specific primers for each species facilitated their detection in comparison with traditional isolation methods. More information is necessary to understand the molecular mechanisms involved in the complex role that bacterial communities may play in the development of cancer (and vice versa).

Marine Actinomycetes as potential source for histone deacetylase inhibitors and epigenetic modulation.

UNLABELLED: In the light of important detrimental role of aberrant histone deacetylases (HDAC) production during various clinical complications, development of therapeutically effective and specific inhibitors of HDAC is critically important. This study deals with the screening for HDAC inhibitors from marine Actinomycetes. The isolation of Actinomycetes from 22 sediment samples along the Southern Coast of India yielded 186 strains including Streptomyces, Nocardipsis, evaluated for HDAC inhibition using HeLa cells. Among the 186 isolates, 10 strains have shown moderate to strong inhibition. The maximum inhibition (61%) was seen with strain VITKSM06 and least inhibition (31%) was seen with strain VITSJT03. The MTT cell proliferation assay using HeLa cell line showed significant cytotoxicity with an IC50 of 5·9 µg ml(-1) by VITKSM06-derived metabolite and 26·2 µg ml(-1) by VITSJT03. The compound treated HeLa cells displayed an altered morphology and condensed chromatin which may be due to HDAC inhibition. Based on the phylogenetic analysis, the potential strains were identified as Nocardiopsis sp VITKSM06, Streptomyces sp VITAKS1 and Streptomyces sp VITRSM02. This study reveals the importance of screening marine Actinomycetes for the discovery of potential novel HDAC inhibitors of therapeutic importance. SIGNIFICANCE AND IMPACT OF THE STUDY: Histone deacetylases (HDAC) are epigenetic enzymes that regulate the deacetylation in lysine group on a histone, and thus regulate the gene expression. The HDAC inhibitors are reported to promote apoptosis on tumour cells, thus become clinically important drug target. Several studies have addressed the identification of putative HDAC inhibitors as therapeutic agents for cancer and until now those cleared phase III human trials are very limited. This study attempts to investigate the chemical diversity found in marine Actinomycetes towards negative HDAC modulation, which could be used individually or in combination as anti-cancerous and other therapeutic measure.

Pseudo-outbreak of Actinomyces graevenitzii associated with bronchoscopy.

Outbreaks and pseudo-outbreaks of infection related to bronchoscopy typically involve Gram-negative bacteria, Mycobacterium species or Legionella species. We report an unusual bronchoscopy-related pseudo-outbreak due to Actinomyces graevenitzii. Extensive epidemiological and microbiological investigation failed to identify a common source. Strain typing revealed that the cluster was comprised of heterogeneous strains of A. graevenitzii. A change in laboratory procedures for Actinomyces cultures was coincident with the emergence of the pseudo-outbreak, and we determined that A. graevenitzii isolates more readily adopted a white, dry, molar tooth appearance on anaerobic colistin nalidixic acid (CNA) agar which likely facilitated its detection and identification in bronchoscopic specimens. This unusual pseudo-outbreak was related to frequent requests of bronchoscopists for Actinomyces cultures combined with a change in microbiology laboratory practices.

Lethality of sortase depletion in Actinomyces oris caused by excessive membrane accumulation of a surface glycoprotein.

Sortase, a cysteine-transpeptidase conserved in Gram-positive bacteria, anchors on the cell wall many surface proteins that facilitate bacterial pathogenesis and fitness. Genetic disruption of the housekeeping sortase in several Gram-positive pathogens reported thus far attenuates virulence, but not bacterial growth. Paradoxically, we discovered that depletion of the housekeeping sortase SrtA was lethal for Actinomyces oris; yet, all of its predicted cell wall-anchored protein substrates (AcaA-N) were individually dispensable for cell viability. Using Tn5-transposon mutagenesis to identify factors that upend lethality of srtA deletion, we uncovered a set of genetic suppressors harbouring transposon insertions within genes of a locus encoding AcaC and a LytR-CpsA-Psr (LCP)-like protein. AcaC was shown to be highly glycosylated and dependent on LCP for its glycosylation. Upon SrtA depletion, the glycosylated form of AcaC, hereby renamed GspA, was accumulated in the membrane. Overexpression of GspA in a mutant lacking gspA and srtA was lethal; conversely, cells overexpressing a GspA mutant missing a membrane-localization domain were viable. The results reveal a unique glycosylation pathway in A. oris that is coupled to cell wall anchoring catalysed by sortase SrtA. Significantly, this novel phenomenon of glyco-stress provides convenient cell-based assays for developing a new class of inhibitors against Gram-positive pathogens.

Glycomyces fuscus sp. nov. and Glycomyces albus sp. nov., actinomycetes isolated from a hypersaline habitat.

Two actinomycete strains, designated TRM 49117(T) and TRM 49136(T), were isolated from a hypersaline habitat in Xinjiang Province, north-west China and were characterized taxonomically by using a polyphasic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TRM 49117(T) had 93.93% similarity with the type strain Glycomyces halotolerans TRM 40137(T) (GenBank accession no. HQ651156) and TRM 49136(T) had 94.32% similarity with G. halotolerans TRM 40137(T). The 16S rRNA gene sequence similarity between the two new isolates was 93%. The isolates contained meso-diaminopimelic acid as the diagnostic diamino acid and anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major cellular fatty acids. The predominant menaquinones of the isolates were MK-9(H4) and MK-9(H6). The whole-cell sugar patterns of these strains contained xylose and ribose, and strain TRM 49136(T) also contained arabinose. The polar lipid pattern of strain TRM 49117(T) comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylcholine, phosphatidylinositol and three additional unknown phospholipids. The polar lipid pattern of strain TRM 49136(T) comprised phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, glycolipids and two phosphoglycolipids of unknown composition. Genotypic and phenotypic data confirmed that strains TRM 49117(T) and TRM 49136(T) represent two novel species, clearly different from related species of the genus Glycomyces, for which the names Glycomyces fuscus sp. nov. (type strain TRM 49117(T) = CCTCC AA 2013003(T) = NRRL B-59998(T) = KACC 17682(T)) and Glycomyces albus sp. nov. (type strain TRM 49136(T) = CCTCC AA 2013004(T) = NRRL B-24927(T) = KACC 17681(T)) are proposed.

Clinical and microbiologic effects of adjunctive metronidazole plus amoxicillin in the treatment of generalized chronic periodontitis: smokers versus non-smokers.

BACKGROUND: The aim of the present study is to evaluate the clinical and microbiologic effects of the adjunctive use of metronidazole (MTZ) and amoxicillin (AMX) in the treatment of smokers and non-smokers with generalized chronic periodontitis (CP). METHODS: Thirty-two smokers and 32 non-smokers were selected and received scaling and root planing (SRP) combined with MTZ (400 mg three times daily) and AMX (500 mg three times daily) for 14 days. Clinical and microbiologic examinations were performed at baseline and 3 months after SRP. Nine subgingival plaque samples per patient were analyzed using checkerboard DNA-DNA hybridization. RESULTS: Both groups presented a significant improvement in all clinical parameters at 3 months after therapy (P <0.05). Non-smokers showed lower mean number of sites with probing depth (PD) ≥5 mm after therapy. Fewer non-smokers exhibited at least nine of these sites at 3 months after treatment. Non-smokers also presented the greatest reductions in mean PD and gain in clinical attachment between baseline and 3 months after therapy at initially deep (PD ≥7 mm) sites (P <0.01). The most beneficial changes in the microbial profile were also observed in the non-smoker group, which showed the lowest proportions of the orange complex at 3 months, as well as a significant increase in the proportions of Actinomyces species after treatment. CONCLUSION: Smokers with CP benefit less than non-smokers from treatment by the combination of SRP, MTZ, and AMX.

The association between detectable plasmatic human immunodeficiency virus (HIV) viral load and different subgingival microorganisms in Brazilian adults with HIV: a multilevel analysis.

BACKGROUND: This study investigates the association between detectable plasmatic human immunodeficiency virus (HIV) viral load (HVL) and high levels of periodontal- and non-periodontal-related microorganisms in the subgingival microbiota of individuals with HIV. METHODS: Thirty-seven individuals with HIV were divided into two groups: 1) detectable HVL (n = 15); and 2) undetectable HVL (n = 22). Subgingival biofilm samples were obtained, and the levels of 35 microbial species were determined by the checkerboard DNA-DNA hybridization method. Periodontal clinical measures and laboratory and sociodemographic data were also registered. χ(2) test, Fisher exact test, and Mann-Whitney U test were used to compare groups. Multilevel ordinal regression models were used to test the association between HVL and the levels of 35 microbial species in subgingival biofilm, adjusted for confounders. RESULTS: Of the 35 species studied, 11 (31.4%) showed higher mean levels in the detectable HVL group than undetectable HVL group (P <0.001). These species included Actinomyces naeslundii II, Actinomyces israelii, Actinomyces odontolyticus, Veillonella parvula, Capnocytophaga gingivalis, Eikenella corrodens, Campylobacter concisus, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Candida albicans. Significant associations between detectable HVL and high levels of microorganisms, adjusted for confounders, were observed for A. naeslundii I, Actinomyces gerencseriae, C. gingivalis, E. corrodens, C. concisus, Prevotella nigrescens, T. forsythia, and Dialister pneumosintes. CONCLUSION: Detectable plasmatic HVL in individuals with HIV was associated with elevated levels of known periodontal pathogens, such as P. nigrescens, T. forsythia, and E. corrodens, as well as C. concisus, C. gingivalis, and D. pneumosintes in the subgingival biofilm.

Identification of the actinomycete 16S ribosomal RNA gene by polymerase chain reaction in oral inflammatory lesions.

OBJECTIVES: To examine the histopathological characteristics of inflammatory lesions containing Actinomyces based on DNA sequencing. Furthermore, case reports of actinomycosis in the maxillofacial region are summarized by a review of the literature. STUDY DESIGN: The study comprised 12 cases of inflammatory lesions containing Actinomyces as diagnosed by DNA analysis. The average age of the subjects was 59 ± 15 years (6 males; 6 females). RESULTS: The distribution of causative bacteria was: Actinomyces israelii in 9 cases, Actinomyces gerencseriae in 2 cases, and Actinomyces naeslundii in 1 case. Four cases diagnosed by DNA sequencing were positive for "Druse," a known morphological diagnostic characteristic of actinomycosis, and 8 cases lacked typical colony formation. CONCLUSIONS: DNA analysis using paraffin-embedded samples is effective for both early and accurate diagnosis of oral lesions containing Actinomyces.

Characterization of oral bacterial diversity of irradiated patients by high-throughput sequencing.

The objective of this study was to investigate the compositional profiles and microbial shifts of oral microbiota during head-and-neck radiotherapy. Bioinformatic analysis based on 16S rRNA gene pyrosequencing was performed to assess the diversity and variation of oral microbiota of irradiated patients. Eight patients with head and neck cancers were involved in this study. For each patient, supragingival plaque samples were collected at seven time points before and during radiotherapy. A total of 147,232 qualified sequences were obtained through pyrosequencing and bioinformatic analysis, representing 3,460 species level operational taxonomic units (OTUs) and 140 genus level taxa. Temporal variations were observed across different time points and supported by cluster analysis based on weighted UniFrac metrics. Moreover, the low evenness of oral microbial communities in relative abundance was revealed by Lorenz curves. This study contributed to a better understanding of the detailed characterization of oral bacterial diversity of irradiated patients.

Suppuration-associated bacteria in patients with chronic and aggressive periodontitis.

BACKGROUND: Suppuration (SUP) on probing may be an indication of active periodontal breakdown. The aim of the present study is to analyze which subgingival species are associated with SUP in patients with chronic (CP) and aggressive (AgP) periodontitis. METHODS: A total of 156 patients with CP and 66 with AgP were submitted to full-mouth periodontal examination and subgingival biofilm sampling (14 sites/patient). The counts of 44 bacterial species were determined by checkerboard. Comparisons between groups and sites were analyzed by the Mann-Whitney and Wilcoxon tests, respectively. Associations between frequency of SUP and bacterial species were analyzed by the Spearman correlation coefficient. RESULTS: The prevalence of SUP in patients with CP was 24.4%, and in patients with AgP it was 30.3%, and the percentage of SUP sites in the groups was 5.72% ± 1.06% and 6.96% ± 1.70%, respectively (P >0.05). SUP sites from patients with CP had significantly higher counts of Veillonella parvula, Dialister pneumosintes, Tannerella forsythia, and Prevotella nigrescens than SUP sites from patients with AgP (P <0.005). Significant positive correlations between high frequency of SUP and high levels of Actinomyces spp, Streptococcus spp., members of the orange complex, Acinetobacter baumannii, and Pseudomonas aeruginosa were observed in patients with CP (P <0.05). In patients with AgP, Actinomyces oris, Propionibacterium acnes, P. aeruginosa, Staphylococcus aureus, and Streptococcus sanguinis were positively associated with SUP, whereas Prevotella intermedia presented a negative association with SUP (P <0.05). CONCLUSIONS: SUP sites from patients with CP harbored significantly higher counts of several periodontal species than SUP sites from patients with AgP. Actinomyces spp., Streptococcus spp., members of the orange complex, T. forsythia, and certain non-oral pathogens were associated with a high number of sites with SUP.

Pulmonary Actinomyces graevenitzii infection presenting as organizing pneumonia diagnosed by PCR analysis.

We report what is believed to be the first case of pulmonary Actinomyces graevenitzii infection presenting as organizing pneumonia. Fever and night sweats developed in a 69-year-old male. The only abnormal laboratory data were an elevated erythrocyte sedimentation rate and C-reactive protein level. On chest images, multiple consolidations with air bronchograms were seen in the bilateral lungs. Histological examination from lung biopsy revealed a pattern of organizing pneumonia with microabscesses, but definitive diagnosis was not obtained because culture from lung specimen was negative. A. graevenitzii was eventually identified in the lung biopsy specimen by detection of an Actinomyces-specific PCR product followed by 16S rRNA gene sequencing. The patient was treated with high-dose ampicillin intravenously for 1 month, followed by oral amoxicillin and clarithromycin for 6 months, and recovered. We suggest that actinomycosis can present as organizing pneumonia, and identification of infection by PCR analysis and rRNA gene sequencing is a useful strategy in cases that are difficult to diagnose.

Bacterial diversity in the saliva of patients with different oral hygiene indexes

The objective of the present study was to evaluate the bacterial diversity in the saliva of patients with different oral hygiene indexes using of two 16S rRNA gene libraries. Each library was composed of samples from patients with different averages of the differentiated Silness-Löe biofilm index: the first library (A) with an index between 1.0 and 3.0 (considered a high index) and the second library (B) between 0 and 0.5 (considered a low index). Saliva DNA was extracted and the 16S rRNA gene was amplified and cloned. The obtained sequences were compared with those stored at NCBI and RDP GenBank. The saliva of patients with high index presented five known genera - Streptococcus, Granulicatella, Gemella, Veillonella and Peptostreptococcus - and 33.3% of nonculturable bacteria grouped into 23 operational taxonomic units (OTUs). The saliva of patients with low index differed significantly from the first library (p=0.000) and was composed of 42 OTUs distributed into 11 known genera - Streptococcus, Granulicatella, Gemella, Veillonella, Oribacterium, Haemophilus, Escherichia, Neisseria, Prevotella, Capnocytophaga, Actinomyces - including 24.87% of nonculturable bacteria. It was possible to conclude that there is greater bacterial diversity in the saliva of patients with low dental plaque in relation to patients with high dental plaque.

O objetivo do presente estudo foi avaliar a diversidade bacteriana da saliva de pacientes com diferentes índices de higiene bucal através da construção de duas bibliotecas do gene 16S rRNA. Cada biblioteca foi composta por amostras de saliva de pacientes com índice de biofilme dental de Silness-Löe diferenciado, sendo a primeira (A) com índice de 1,0 a 3,0 (denominada de alto índice) e a segunda (B), entre 0 a 0,5 (denominada de baixo índice). O DNA da saliva foi extraído e o gene 16S rRNA foi amplificado, clonado e sequenciado. As sequências obtidas foram comparadas com aquelas armazenadas no GenBank do NCBI e RDP. A saliva de pacientes com alto índice de biofilme dental apresentou cinco gêneros conhecidos: Streptococcus, Granulicatella, Gemella, Veillonella e Peptostreptococcus e 33,3% de bactérias não-cultivadas, agrupados em 23 unidades taxonômicas operacionais (UTOs). A saliva de pacientes com baixo índice de biofilme dental, foi diferente significativamente da primeira (p=0,000) e foi composta de 42 UTOs, distribuídas em 11 gêneros conhecidos: Streptococcus, Granulicatella, Gemella, Veillonella, Oribacterium, Haemophilus, Escherichia, Neisseria, Prevotella, Capnocytophaga, Actinomyces, além de 24,87% de bactérias não-cultivadas. Pode-se concluir que existe maior diversidade bacteriana na saliva de pacientes com baixo índice de biofilme dental em relação a pacientes com alto índice de biofilme dental.

Identification and treatment of bisphosphonate-associated actinomycotic osteonecrosis of the jaws.

Osteonecrosis of the jaws (ONJ) is a condition characterized by necrotic exposed bone in the jaws of patients receiving intravenous or oral bisphosphonate therapy. A review of the medical and dental literature reveals that the pathoetiology of ONJ remains unknown and there is no established link that bisphosphonates are the primary cause of this bone pathology. However, there is clinical evidence that Actinomyces may play a critical role in the pathogenesis of bisphosphonate-associated ONJ. Identification and a prolonged course of oral antimicrobial therapy may lead to complete resolution of this actinomycotic osteonecrosis.