Differential flora in the microenvironment of lung tumor and paired adjacent normal tissues.

Recent evidence demonstrates the existence of diversified microbiota in the lung. However, the effect of lung carcinogenesis on the flora in lung microenvironment has yet not been well investigated. In this study, we surveyed the microbial composition and diversity in lung tumor and paired adjacent normal tissues obtained from 55 lung cancer patients to test whether any specific tumor-associated microbial features in lung microenvironment can be identified. Compared with non-malignant adjacent tissues, the tumor samples showed significantly lower community richness (α diversity), but no significant difference in overall microbiome dissimilarity (ß diversity). Strong intrasubject correlations were observed between tumor sample and its paired non-malignant adjacent tissues. In addition, correlation network analysis found more significant taxa-taxa correlations (adjusted q-value < 0.05) in tumor microenvironment than non-malignant adjacent tissues. At taxa level, we found Propionibacterium genus were significantly reduced in tumor tissues compared with non-malignant adjacent tissues. In summary, the microbiota in tumor tissues showed the lower richness, higher taxa-taxa interaction, and reduction of potential pro-inflammatory microbial genera compared with non-malignant tissues, suggesting the potential link between the tumor microbiota and the altered tumor microenvironment for the further investigation.

Clinical and Biological Features of Cutibacterium (Formerly Propionibacterium) avidum, an Underrecognized Microorganism.

The recent description of the genus Cutibacterium has altered the taxonomy of Propionibacterium species. These organisms still belong to the genera of the skin coryneform group, and the most-studied species remains Cutibacterium acnes. Cutibacterium avidum is also a known skin commensal. This underrecognized microorganism can, however, act as a pathogen after bacterial seeding and can be considered opportunistic, causing either superficial or deep/invasive infections. It can cause numerous infections, including but not limited to breast infections, skin abscesses, infective endocarditis, and device-related infections. The ecological niche of C. avidum is clearly different from that of other members of the genus: it is found in the axillary region or at wet sites rather than in dry, exposed areas, and the number of microorganisms increases during puberty. Historically, it has been used for its ability to modulate the immune response and for its antitumor properties. Conventional microbial culture methods and identification processes allow for its accurate identification and characterization. Thanks to the modern omics tools used for phylogenomic approaches, understanding C. avidum pathogenesis (including host-bacterium interactions and virulence factor characterization) is becoming easier, allowing for more thorough molecular characterization. These analyses have revealed that C. avidum causes diverse diseases mediated by multiple virulence factors. The recent genome approach has revealed specific genomic regions within this species that are involved in adherence and biofilm formation as well as fitness, survival, and defense functions. Numerous regions show the presence of phages and horizontal gene transfer. C. avidum remains highly sensitive to a broad spectrum of antibiotics, such as ß-lactams, fluoroquinolones, macrolides, and rifampin, although erythromycin and clindamycin resistance has been described. A long-term treatment regimen with a combination of antibiotics is required to successfully eliminate the remaining adherent bacteria, particularly in the case of deep infections after debridement surgery.

Propionibacterium namnetense sp. nov., isolated from a human bone infection.

A polyphasic taxonomic study was performed on two Gram-positive-staining, anaerobic, pleomorphic, rod-shaped strains isolated from human bone and tissue samples. Sequencing of the 16S rRNA genes revealed that the strains belong to a novel species within the genus Propionibacterium, most closely related to Propionibacterium acnes subsp. acnes and Propionibacterium acnes subsp. elongatum with similarity values of 98.4 % and 98.1 %, respectively. In addition, protein-coding genes for rpoB, recA and gyrB clearly separated the novel organism from all species and subspecies of the genus Propionibacterium. However, a DNA-DNA hybridization analysis between the novel organism and the type strain P. acnes ATCC 6919T revealed a value of only 61.1 %. Furthermore, whole genome analysis using the program OrthoANI gave a value of 88.5 %, which is significantly below the cut-off value of 95 % for species delineation. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0. The DNA G+C content of the type strain was 59.7 mol%. When taken collectively, phenotypic, molecular genetic, chemotaxonomic and phylogenetic information demonstrate that the organism represents a distinct, albeit close relative of P. acnes On the basis of the results presented, the organism represents a novel member of the genus Propionibacterium for which the name Propionibacterium namnetense sp. nov. is proposed. The type strain is NTS 31307302T (=DSM 29427T=CCUG 66358T).

Real-time quantitative reverse transcription-polymerase chain reaction to detect propionibacterial ribosomal RNA in the lymph nodes of Chinese patients with sarcoidosis.

The aim of this study was to investigate the diagnostic value of using the copy number of propionibacterial rRNA as a biomarker for sarcoidosis. Ribosomal RNA of Propionibacterium acnes and P. granulosum was measured by real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) using formalin-fixed and paraffin-embedded tissue of lymph node biopsy from 65 Chinese patients with sarcoidosis, 45 with tuberculosis and 50 controls with other diseases (23 with non-specific lymphadenitis and 27 with mediastinal lymph node metastasis from lung cancer). The receiver operating characteristic (ROC) curve was analysed to determine an optimal cut-off value for diagnosis, and the diagnostic accuracy of the cut-off value was evaluated in additional tissue samples [24 patients with sarcoidosis and 22 with tuberculosis (TB)]. P. acnes or P. granulosum rRNA was detected in 48 of the 65 sarcoidosis samples but only in four of the 45 TB samples and three of the 50 control samples. Analysis of the ROC curve revealed that an optimal cut-off value of the copy number of propionibacterial rRNA for diagnosis of sarcoidosis was 50·5 copies/ml with a sensitivity and specificity of 73·8 and 92·6%, respectively. Based on the cut-off value, 19 of the 24 additional sarcoidosis samples exhibited positive P. acnes or P. granulosum, whereas only one of the 22 additional TB samples was positive, resulting in a sensitivity and specificity of 79·2 and 95·5%, respectively. These findings suggest that propionibacteria might be associated with sarcoidosis granulomatous inflammation. Detection of propionibacterial rRNA by RT-PCR might possibly distinguish sarcoidosis from TB.

Identification, typing and characterisation of Propionibacterium strains from healthy mucosa of the human stomach.

Forty two Propionibacterium isolates were recovered from biopsy samples of the gastric mucosa of eight out of 12 healthy people. Of these, 41 were identified as belonging to Propionibacterium acnes; the remaining isolate was identified as belonging to Propionibacterium granulosum. Repetitive extragenic palindromic (REP)-PCR typing suggested that up to four strains might be present in the mucosa of the same individual. Sequence analysis of either recA, tly or camp5 genes of P. acnes isolates revealed two distinct phylogenetic lineages. As per the recA, most isolates belonged to type I, while the remainder of the isolates belonged to type II. Phenotypic analyses of representative isolates showed the different strains to have diverse biochemical properties. For example, large differences were seen in carbohydrate fermentation patterns, the results of qualitative and quantitative enzymatic profiling, and survival at acidic pH. In contrast, the patterns of resistance/susceptibility to a series of 16 antibiotics were rather similar, with no atypical resistances observed. The examined strains showed limited-if any-enzymatic activities that could be ultimately related to pathogenicity (lipolytic, proteolytic or haemolytic activity). This suggests that, in the gastric ecosystem, some Propionibacterium spp. genotypes and/or phenotypes can be considered true commensals.

Pelvic actinomycosis-like disease due to Propionibacterium propionicum after hysteroscopic removal of an intrauterine device.

A female patient presented with episodes of fever and pain in the lower right abdomen after hysteroscopic removal of an intrauterine device 2 months earlier. Pelvic actinomycosis originating from a tubo-ovarian abscess was diagnosed with Propionibacterium propionicum, formerly known as Arachnia propionica, as causative agent.

Propionibacterium endocarditis: a case series from the International Collaboration on Endocarditis Merged Database and Prospective Cohort Study.

Propionibacterium species are occasionally associated with serious systemic infections such as infective endocarditis. In this study, we examined the clinical features, complications and outcome of 15 patients with Propionibacterium endocarditis using the International Collaboration on Endocarditis Merged Database (ICE-MD) and Prospective Cohort Study (ICE-PCS), and compared the results to 28 cases previously reported in the literature. In the ICE database, 11 of 15 patients were male with a mean age of 52 y. Prosthetic valve endocarditis occurred in 13 of 15 cases and 3 patients had a history of congenital heart disease. Clinical findings included valvular vegetations (9 patients), cardiac abscesses (3 patients), congestive heart failure (2 patients), and central nervous system emboli (2 patients). Most patients were treated with beta-lactam antibiotics alone or in combination for 4 to 6 weeks. 10 of the 15 patients underwent valve replacement surgery and 2 patients died. Similar findings were noted on review of the literature. The results of this paper suggest that risk factors for Propionibacterium endocarditis include male gender, presence of prosthetic valves and congenital heart disease. The clinical course is characterized by complications such as valvular dehiscence, cardiac abscesses and congestive heart failure. Treatment may require a combination of medical and surgical therapy.

Polymerase chain reaction-based analysis of microorganisms associated with failed endodontic treatment.

OBJECTIVE: In this study, we aimed to investigate the occurrence of several microbial species in cases of failed endodontic therapy by means of the polymerase chain reaction (PCR). Study design Root canal samples were taken from 22 root-filled teeth with persistent periradicular lesions selected for re-treatment. DNA was extracted from the samples and analyzed for the presence of 19 microbial taxa by using the polymerase chain reaction. RESULTS: All samples were positive for at least 1 of the target microbial species. Enterococcus faecalis was the most prevalent species-detected in 77% of the cases. The other most prevalent species were Pseudoramibacter alactolyticus (52%), Propionibacterium propionicum (52%), Dialister pneumosintes (48%), and Filifactor alocis (48%). Candida albicans was found in 9% of the samples. The mean number of species in samples filled up to 2 mm short of the radiographic apex was 3 (range, 1-5), whereas cases in which the filling was greater than 2 mm from the apex yielded a mean of 5 species (range, 2-11). This difference was statistically significant (P <.05). CONCLUSIONS: Microorganisms occurred in all cases of root-filled teeth associated with periradicular lesions, which lends strong support to the assertion that treatment failures are rather of infectious etiology, caused by persistent or secondary intraradicular infections. E faecalis was the most prevalent species, followed by 4 other anaerobic species: P. alactolyticus, P. propionicum, D. pneumosintes, and F. alocis. All examined samples harbored at least 1 of the following gram-positive bacterial species: E. faecalis, P. alactolyticus, or P. propionicum.

Polymerase chain reaction detection of Propionibacterium propionicus and Actinomyces radicidentis in primary and persistent endodontic infections.

OBJECTIVE: Propionibacterium propionicus and the recently described species Actinomyces radicidentis have been isolated from infections of endodontic origin; nevertheless, the possibility exists that their actual prevalence may have been underestimated by culture. The purpose of our study was to assess the occurrence of these 2 species in different types of endodontic infections by using the sensitive 16S rDNA-based nested polymerase chain reaction approach. STUDY DESIGN: To detect these 2 species, nested polymerase chain reaction was performed directly in samples taken from primary endodontic infections associated with asymptomatic periradicular lesions, acute apical periodontitis, or acute periradicular abscesses and in samples from patients in whom endodontic therapy had failed. DNA was extracted from the samples and initially amplified by using universal 16S rDNA primers. In the second round of amplification, the first polymerase chain reaction products were used to detect a specific 16S rDNA fragment of either P propionicus or A radicidentis. RESULTS: P propionicus was detected in 6/21 (29%) root canal samples from teeth with chronic periradicular lesions, in 5/10 (50%) cases diagnosed as acute apical periodontitis, and in 7/19 (37%) pus samples aspirated from acute periradicular abscesses. Overall, this species was found in 18/50 (36%) samples taken from primary endodontic infections. Of the root canal samples obtained from root-filled teeth with chronic periradicular lesions, P propionicus was detected in 7/12 (58%) cases. A radicidentis was detected in 1/21 (5%) root canal samples from teeth with chronic periradicular lesions and in 1/10 (10%) cases of acute apical periodontitis. No pus sample yielded this species. In general, A radicidentis was detected in 2/50 (4%) samples taken from primary endodontic infections and in 1/12 (8%) root canal samples taken from patients in whom endodontic treatment had failed. CONCLUSIONS: P propionicus was found in a relatively large number of patients with primary and persistent endodontic infections. This strengthens the assumption that this bacterial species is an endodontic pathogen associated with different forms of periradicular diseases. In contrast, A radicidentis was only occasionally detected in the patients examined. The role played by this species in endodontic infections remains to be clarified.

The effects of an immediately pre-surgical chlorhexidine oral rinse on the bacterial contaminants of bone debris collected during dental implant surgery.

Dental implant surgery produces bone debris that can be used in the "simultaneous augmentation" technique. Although this debris is contaminated with oral bacteria, a stringent aspiration protocol has been shown to reduce the levels of contamination. Chlorhexidine mouthrinse is a well-proven antibacterial rinse that has been shown to reduce infectious complications associated with dental implants. This study examined the effect of pre-operative rinsing with a 0.1% chlorhexidine digluconate mouthrinse on the bacterial contaminants present in collected bone debris bone (CBD). Twenty partially edentate patients were randomly allocated into equal groups and underwent bone collection using the Frios Bone Collector (FBC) during the insertion of two dental implants. In group T a pre-operative chlorhexidine rinse was used, whilst in group C sterile water was used. For both groups, a stringent bone collection protocol was used. Bone samples were immediately transported for microbial analysis. Colonial and microscopic morphology, gaseous requirements and identification kits were utilised for identification of the isolated microbes. Thirty-nine species were identified including a number associated with disease, in particular Actinomyces odontolyticus, Clostridium bifermentans, Prevotella intermedia, and Propionibacterium propionicum. Samples from group T (chlorhexidine mouthrinse) yielded significantly fewer organisms (P < 0.001) than in group C (sterile water mouthrinse). Gram-positive cocci dominated the isolates from both groups. It is concluded that if bone debris is to be used for the purpose of immediate simultaneous augmentation, a preoperative chlorhexidine mouthrinse should be utilised in conjunction with a stringent aspiration protocol to reduce further the bacterial contamination of CBD.

Quantitative analysis of mycobacterial and propionibacterial DNA in lymph nodes of Japanese and European patients with sarcoidosis.

The cause(s) of sarcoidosis is unknown. Mycobacterium spp. are suspected in Europe and Propionibacterium spp. are suspected in Japan. The present international collaboration evaluated the possible etiological links between sarcoidosis and the suspected bacterial species. Formalin-fixed and paraffin-embedded sections of biopsy samples of lymph nodes, one from each of 108 patients with sarcoidosis and 65 patients with tuberculosis, together with 86 control samples, were collected from two institutes in Japan and three institutes in Italy, Germany, and England. Genomes of Propionibacterium acnes, Propionibacterium granulosum, Mycobacterium tuberculosis, Mycobacterium avium subsp. paratuberculosis, and Escherichia coli (as the control) were counted by quantitative real-time PCR. Either P. acnes or P. granulosum was found in all but two of the sarcoid samples. M. avium subsp. paratuberculosis was found in no sarcoid sample. M. tuberculosis was found in 0 to 9% of the sarcoid samples but in 65 to 100% of the tuberculosis samples. In sarcoid lymph nodes, the total numbers of genomes of P. acnes or P. granulosum were far more than those of M. tuberculosis. P. acnes or P. granulosum was found in 0 to 60% of the tuberculosis and control samples, but the total numbers of genomes of P. acnes or P. granulosum in such samples were less than those in sarcoid samples. Propionibacterium spp. are more likely than Mycobacteria spp. to be involved in the etiology of sarcoidosis, not only in Japanese but also in European patients with sarcoidosis.

Identification of anaerobic nonsporeforming gram-positive bacilli by biochemical tests and gas-liquid chromatography.

There are many methods to identify anaerobic nonsporeforming bacilli: histological, bacteriological (biochemical test, microsystem API 20 A), serological, cell wall composition analysis, molecular methods and gas-liquid chromatography (GLC). A comparison between biochemical tests and gas-liquid chromatography was made in this study for the identification of this group of microorganisms. GLC conditions were established with the aid of reference strains. These conditions were then applied to ten strains which were previously identified by biochemical tests. Strains were grown in PYG broth and fermentation end products were analyzed, volatile and non volatile fatty acids. Their qualitative determination was made by comparing the retention time of known standards and the chromatographic pattern of reference strains. In addition, a semiquantitative analysis was made. The results of identification by biochemical tests were: five strains belonged to Actinomyces genus; three were Propionibacterium acnes; one Propionibacterium granulosum and one P. propionicum. By the GLC only seven strains were identified: four were Actinomyces and three P. acnes. Only six strains showed identification correlation by both biochemical tests and GLC. GLC is a presumptive identification method that can be used along with other complementary tests for a definitive identification at genus level.

Gas-liquid chromatography of bacterial fatty acids with a fused-silica capillary column.

The use of flexible, fused-silica capillary column for gas-liquid chromatographic analysis of bacterial fatty acids is illustrated with Propionibacterium acnes, Propionibacterium shermanii, and a standard methyl ester mixture.