Bacterial Skin Dysbiosis in Darier Disease.

INTRODUCTION: Darier disease is a rare inherited disease with dominant skin manifestations including keratotic papules and plaques on sebaceous and flexural areas. Secondary infection of skin lesions is common, and Staphylococcus aureus commonly colonizes these lesions. The aim of the study was to characterize the bacterial microbiome of cutaneous Darier lesions compared to normal-looking skin and disease severity. METHODS: All patients with a history of Darier followed up at Emek Medical Center were invited to participate in the study. Patients that did not use antibiotics in the past month and signed informed consent had four skin sites sampled with swabs: scalp, chest, axilla, and palm. All samples were analyzed for bacterial microbiome using 16S rDNA sequencing. RESULTS: Two hundred and eighty microbiome samples obtained from lesional and non-lesional skin of the scalp, chest, axilla, and palm of 42 Darier patients were included in the analysis. The most abundant bacterial genera across all skin sites were Propionibacterium, Corynebacterium, Paracoccus, Micrococcus, and Anaerococcus. Scalp and chest lesions featured a distinct microbiome configuration that was mainly driven by an overabundance of Staphylococci species. Patients with more severe disease exhibited microbiome alterations in the chest, axilla, and palm compared with patients with only mild disease, driven by Peptoniphilus and Moryella genera in scalp and palmar lesions, respectively. CONCLUSION: Staphylococci were significantly associated with Darier lesions and drove Darier-associated dysbiosis. Severity of the disease was associated with two other bacterial genera. Whether these associations also hold a causative role and may serve as a therapeutic target remains to be determined and requires further investigation.

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.

Misidentification of Cutibacterium namnetense as Cutibacterium acnes among clinical isolates by MALDI-TOF VitekMS: usefulness of gyrB sequencing and new player in bone infections.

The taxonomy modification of Propionibacterium sp. with the description of new species, especially Cutibacterium namnetense, raises the question of species distribution in routine clinical samples. We performed a retrospective study during 3 years before the implementation of MALDI-TOF. Two hundred sixty-nine isolates were included in the study. MALDI-TOF identification, 16S rRNA, and new developed gyrB partial sequencings were performed. The most representative species was C. acnes in 88% of the cases, regardless of the origin of the clinical sample. Eventually, we identified three C. namnetense strains, representing a 1.1% prevalence over the period of time, including two bone infections. MALDI-TOF databases should be regularly updated to incorporate new species. gyrB sequencing constitutes a both easy and relevant method to identify Cutibacterium sp. especially C. namnetense, a new player in bone infections.

Psoriatic lesions are characterized by higher bacterial load and imbalance between Cutibacterium and Corynebacterium.

BACKGROUND: Several studies have found that the microbiota of psoriatic lesions is different from that of healthy skin. OBJECTIVE: To characterize the microbiota of lesional and unaffected skin in patients with psoriasis and controls and investigate the correlation between cutaneous microbiota and clinical features of psoriasis. METHODS: Using quantitative polymerase chain reaction and 16S rRNA sequencing, we assayed the profiles of cutaneous microbiota in controls, unaffected skin, and psoriatic lesions. We also investigated the correlation of psoriasis-associated taxa with clinical characteristics. RESULTS: High bacterial load was identified in the psoriatic lesions compared with unaffected skin and controls. There was an imbalance between Cutibacterium (also known as Propionibacterium) and Corynebacterium in psoriatic skin. Lesions showed a higher proportion of Corynebacterium and a lower proportion of Cutibacterium compared with unaffected skin and controls. Corynebacterium was correlated with the severity of local lesions, whereas Cutibacterium showed correlation with the abnormity of skin capacitance. LIMITATIONS: We did not conduct a longitudinal study. CONCLUSIONS: Psoriatic lesions are characterized by higher bacterial load and imbalance between Cutibacterium and Corynebacterium.

Nocardioides jejuensis sp. nov., isolated from soil.

A Gram-stain positive, asporogenous, aerobic, white -coloured bacterium, designated 18JY15-6T, was isolated from soil from Jeju Island, Korea. Pairwise analysis of the 16S rRNA gene sequence of strain 18JY15-6T indicated high similarity to Nocardioides phosphati DSM 104026T (97.4%), Marmoricola terrae KACC 17308T (96.7%) and Nocardioides jensenii KCTC 0074BPT (96.6%). Phylogenetic analysis revealed that strain 18JY15-6T formed a distinct lineage within the family Nocardioidaceae and is closely related to members of the genus Nocardioides. Genome sequencing of strain 18JY15-6T revealed 3221 total genes, including 3162 protein coding genes, 59 RNA and 31 pseudogenes. Growth was observed at 18-37 °C (optimal 30 °C) in R2A medium at pH 7.0. The major cellular fatty acids of strain 18JY15-6T were identified as C16:0, C18:1ω9c, C18:0 10-methyl, tuberculostearic and C17:0. The fatty acid profile of strain 18JY15-6T was more dissimilar when compared with M. terrae. The only respiratory quinone present was found to be MK-8(H4). The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The results of phylogenetic, biochemical and chemotaxonomic characterisation allow the differentiation of strain 18JY15-6T from N. phosphati WYH11-7T, M. terrae JOS5-1T and N. jensenii NBRC 14755T which supports the conclusion that this strain represents a novel species of the genus Nocardioides, for which we propose the name Nocardioides jejuensis sp. nov. The type strain of Nocardioides jejuensis is 18JY15-6T (= KCTC 49105T = JCM 33182T).

Seborrheic dermatitis-Looking beyond Malassezia.

Seborrhoeic Dermatitis (SD) is a very common chronic and/or relapsing inflammatory skin disorder whose pathophysiology remains poorly understood. Yeast of the genus Malassezia has long been regarded as a main predisposing factor, even though causal relationship has not been firmly established. Additional predisposing factors have been described, including sebaceous activity, host immunity (especially HIV infection), epidermal barrier integrity, skin microbiota, endocrine and neurologic factors, and environmental influences. Genetic studies in humans and mouse models-with particularly interesting insights from examining the Mpzl3 knockout mice and their SD-like skin phenotype, and patients carrying a ZNF750 mutation-highlight defects in host immunity, epidermal barrier and sebaceous activity. After synthesizing key evidence from the literature, we propose that intrinsic host factors, such as changes in the amount or composition of sebum and/or defective epidermal barrier, rather than Malassezia, may form the basis of SD pathobiology. We argue that these intrinsic changes provide favourable conditions for the commensal Malassezia to over-colonize and elicit host inflammatory response. Aberrant host immune activity or failure to clear skin microbes may bypass the initial epidermal or sebaceous abnormalities. We delineate specific future clinical investigations, complemented by studies in suitable SD animal models, that dissect the roles of different epidermal compartments and immune components as well as their crosstalk and interactions with the skin microbiota during the process of SD. This research perspective beyond the conventional Malassezia-centric view of SD pathogenesis is expected to enable the development of better therapeutic interventions for the management of recurrent SD.

Propionibacterium ruminifibrarum sp. nov., isolated from cow rumen fibrous content.

A novel propionate producing bacterium, strain JV5T, was isolated from the rumen fibrous content of a Holstein Friesian dairy cow. Cells of strain JV5T were Gram-stain-positive, non-motile and aerotolerant. Growth occurred between 35 and 45 °C, with an optimum at 39 °C. The pH range for growth was 6.5-8, with an optimum at pH 7. The 16S rRNA gene sequence of strain JV5T was 98.4 and 96.5 % identical to those of Propionibacterium australiense DSM 15818T and Propionibacterium acidifaciens DSM 21887T, respectively. Genome wide average nucleotide identity and digital DNA-DNA hybridization values were 88.3 and 35.5 %, respectively, against P. australiense DSM 15818T. The G+C content of strain JV5T was 68.9  mol%. Strain JV5T did not produce urease and was able to metabolize glutamate, but not aspartate and glycine. Strain JV5T was able to ferment a range of substrates including certain simple and complex carbohydrates, sugar alcohols and amino acids. Chemotaxonomic analysis of strain JV5T revealed the presence of meso-diamino pimelic acid isomers similar those found in P. australiense, but different from P. acidifaciens. The observed major (>10 %) cellular fatty acids in strain JV5T (C18 : 1 ω9c, anteiso-C15 : 1, C16 : 0, C17 : 0 and C16 : 0 alcohol) were also different from those observed in P. australiense and P. acidifaciens. Based on these findings, a novel species is proposed within the genus Propionibacterium, Propionibacterium ruminifibrarum sp. nov. (type strain JV5T=DSM 106771T=TISTR 2629T).

C-reactive protein misdiagnoses delayed postoperative spinal implant infections in patients with low-virulent microorganisms.

PURPOSE: C-reactive protein (CRP) has been shown to be a powerful parameter for detecting acute postoperative spinal implant infections (PSII) with a high sensitivity and specificity. However, little data are available on the performance of CRP in the diagnosis of delayed PSII. The aim of the current study was therefore to establish cutoff values for diagnosing delayed infection based on serum CRP. METHODS: All patients who underwent a revision surgery after instrumented spinal fusion from January 2013 through January 2016 were included. Demographic data, laboratory values, type of infection (including microbiological and pathological results), comorbidities and clinical manifestation were collected. The European Bone and Joint Infection Society criteria, proposed to diagnose periprosthetic joint infection, were used to diagnose PSII. RESULTS: A total of 257 patients were included. PSII was diagnosed in 61 patients, representing 24% of the study cohort. There was a significant difference in serum CRP levels between septic and aseptic cohorts (19.3 vs. 4.8 mg/l, p < 0.001). However, 26 patients (43%) from the PSII group had a normal (< 5 mg/l) serum CRP level prior to revision surgery. According to the ROC curve, a serum CRP threshold of 4.05 mg/l had a sensitivity of 64% and specificity of 68%. The most common isolated microorganism was Propionibacterium spp. followed by coagulase-negative staphylococci. CONCLUSION: Serum CRP showed low sensitivity and specificity for diagnosis of delayed PSII, even after applying cutoffs optimized by using receiver operating curve analysis, because of the high incidence of low-virulent pathogens. These slides can be retrieved under Electronic Supplementary Material.

Synthesis of prebiotic galactooligosaccharides from lactose and lactulose by dairy propionibacteria.

The potential of probiotic bacteria to produce prebiotic oligosaccharides by transgalactosylation has been minimally studied. In this work, we screened the ß-galactosidase (ß-gal) activity of dairy propionibacteria (PAB) isolated from Argentinean foods to select strains for the synthesis of oligosaccharides from lactose (GOS) and lactulose (OsLu). PAB, when grown in a medium with lactose as a carbon source, were disrupted, and the cell-free extracts were assayed for ß-gal activity. Nine strains grew on lactose and showed ß-gal activities from 0.27 to 2.60 U mL-1. Propionibacterium acidipropionici LET 120, the strain with the highest activity, was able to synthesize, using 30% lactose and lactulose at pH 6.5 and 45 °C, 26.8% of LET 120-GOS and 26.1% of LET 120-OsLu after 24 h. When they were tested as carbon sources for growth, P. acidipropionici LET 120 attained higher biomasses, µmax and ß-gal activities at the expense of Aspergillus oryzae-OsLu, Vivinal®-GOS and lactulose compared to lactose or glucose. In addition, LET 120-GOS and LET 120-OsLu synthesized by PAB were prebiotic for some probiotic strains. For the first time, our results show the production of GOS and OsLu by dairy PAB, and these results encourage further studies on the optimization of the synthesis and structure characterization of the obtained oligosaccharides.

Skin and soft tissue infection caused by Cutibacterium (formerly Propionibacterium) avidum: Report of eleven cases.

We describe the characteristics of 11 cases of skin and soft tissue infections due to Cutibacterium (formerly Propionibacterium) avidum. This microorganism should be considered a potential skin pathogen especially in patients with breast infections. The clinical outcome is usually good but serious infections such as necrotizing infections may occur.

Propionibacterium avidum: A Virulent Pathogen Causing Hip Periprosthetic Joint Infection.

Background: Propionibacteria are important members of the human skin microbiota, but are also opportunistic pathogens associated with periprosthetic joint infection (PJI). While the role of Propionibacterium acnes in PJI has been widely described, insight into the capacity of Propionibacterium avidum to cause PJI is limited. Methods: An unusual cluster of 4 hip PJIs caused by P. avidum in one orthopedic center in 2015 prompted us to retrospectively identify and analyze clinical data related to previous P. avidum PJI cases (1997-2015). We also characterized the hemolytic and biofilm-producing capacity of our 4 clinical P. avidum strains isolated in 2015, and investigated their phylogenetic relationships by whole-genome sequencing. Results: We retrospectively identified 13 P. avidum PJIs, with the majority being hip-related infections (n = 11). Preoperative synovial fluid cultures were P. avidum positive in 63.6% of cases. Six of 12 patients (50%) with available case histories were treated with an exchange of the prosthesis. In all but 1 of the 6 patients treated with debridement-retention of the prosthesis, treatment failed, thus requiring a 2-stage revision. The isolated P. avidum strains showed a more pronounced hemolytic activity, but a similar biofilm-forming ability when compared to P. acnes. Whole-genome sequencing identified 2 phylogenetic clusters highly related to P. avidum PJI strains isolated in Sweden. Conclusions: We describe the largest series of P. avidum PJI predominantly located in the hip. Phylogenetic similarity of our P. avidum strains to PJI strains isolated elsewhere suggests that these invasive lineages may be common.

Characterisation of the nasal microbiota in granulomatosis with polyangiitis.

OBJECTIVES: Prior studies have suggested a potential link between nasal microbes and granulomatosis with polyangiitis (GPA; Wegener's), but these studies relied on culture-dependent methods. This study comprehensively examined the entire community of nasal microbiota (bacteria and fungi) in participants with GPA compared with healthy controls using deep sequencing methods. METHODS: 16S rRNA and internal transcribed spacer gene sequencing were performed on nasal microbial DNA isolated from nasal swabs of 60 participants with GPA and 41 healthy controls. Alpha and beta diversity were assessed as well as the relative abundance of the most abundant bacterial and fungal taxa. The effects of covariates including disease activity and immunosuppressive therapies on microbial composition were evaluated. RESULTS: Compared with controls, participants with GPA had a significantly different microbial composition (weighted UniFrac p=0.04) and lower relative abundance of Propionibacterium acnes and Staphylococcus epidermidis (for both, false discovery rate-corrected p=0.02). Disease activity in GPA was associated with a lower abundance of fungal order Malasseziales compared with participants with GPA in remission (p=0.04) and controls (p=0.01). Use of non-glucocorticoid immunosuppressive therapy was associated with 'healthy' nasal microbiota while participants with GPA who were off immunosuppressive therapy had more dysbiosis (weighted UniFrac p=0.01). No difference in the relative abundance of Staphylococcus aureus was observed between GPA and controls. CONCLUSIONS: GPA is associated with an altered nasal microbial composition, at both the bacterial and fungal levels. Use of immunosuppressive therapies and disease remission are associated with healthy microbial communities.

Acidipropionibacterium virtanenii sp. nov., isolated from malted barley.

A Gram-stain-positive, catalase-positive and pleomorphic rod organism was isolated from malted barley in Finland, classified initially by partial 16S rRNA gene sequencing and originally deposited in the VTT Culture Collection as a strain of Propionibacterium acidipropionici (currently Acidipropionibacterium acidipropionici). The subsequent comparison of the whole 16S rRNA gene with other representatives of the genus Acidipropionibacterium revealed that the strain belongs to a novel species, most closely related to Acidipropionibacterium microaerophilum and Acidipropionibacterium acidipropionici, with similarity values of 98.46 and 98.31 %, respectively. The whole genome sequencing using PacBio RS II platform allowed further comparison of the genome with all of the other DNA sequences available for the type strains of the Acidipropionibacterium species. Those comparisons revealed the highest similarity of strain JS278T to A. acidipropionici, which was confirmed by the average nucleotide identity analysis. The genome of strain JS278T is intermediate in size compared to the A. acidipropionici and Acidipropionibacterium jensenii at 3 432 872 bp, the G+C content is 68.4 mol%. The strain fermented a wide range of carbon sources, and produced propionic acid as the major fermentation product. Besides its poor ability to grow at 37 °C and positive catalase reaction, the observed phenotype was almost indistinguishable from those of A. acidipropionici and A. jensenii. Based on our findings, we conclude that the organism represents a novel member of the genus Acidipropionibacterium, for which we propose the name Acidipropionibacteriumvirtanenii sp. nov. The type strain is JS278T (=VTT E-113202T=DSM 106790T).

Temporal instability of the post-surgical maxillary sinus microbiota.

BACKGROUND: Chronic rhinosinusitis is an inflammatory disorder in which the role of bacteria remains uncertain. While sinus outflow obstruction is often an initiating event, mucosal inflammation and dysbiosis may persist or develop in sinuses with widely patent surgical openings. Understanding of the relationship between dysbiosis and chronic sinus inflammation is obfuscated by inter-individual microbiota variability and likely intra-individual temporal variation that has yet to be defined. In this study, long-term microbiota stability is investigated within surgically-opened maxillary sinuses of individuals with and without sinus inflammatory disease. METHODS: Maxillary sinus swabs were performed in 35 subjects with longstanding maxillary antrostomies. Subjects with and without active chronic maxillary sinusitis were included. Repeat swabs were obtained from the same sinuses after a prolonged interval (mean 719 ± 383 days). Patients were categorized based on the inflammatory status of the sinus mucosa at times of sample collection, as assessed by nasal endoscopy. Total DNA from swab eluents was extracted, and the microbiota characterized using 16S rRNA gene sequencing followed by taxonomic classification. Prevalence and abundance of genera were determined by analysis of 16S rRNA gene sequences. Taxa were identified that were stably present between two time points in individual subjects. RESULTS: The overall proportion of stable taxa across time points was 24.5 ± 10.6%. This stability index was consistent across patient groups and not correlated with clinical parameters. Highly prevalent taxa, including Staphylococcus, Corynebacterium, Propionibacterium, and Pseudomonas, were often stably present, but varied in relative abundance. Janthinobacterium, Enterobacter, Lactobacillus, and Acinetobacter were prevalent and moderately abundant taxa in healthy sinuses, but not in inflamed sinuses. Moraxella and Haemophilus were present at low prevalence and proportional abundance in chronically or intermittently inflamed sinuses, but not in healthy sinuses. CONCLUSIONS: A relatively small component of the post-antrostomy maxillary sinus microbiota exhibits long-term stability in individual subjects. Stable bacteria include a limited number of highly prevalent and a larger number of lower prevalence taxa, which vary widely in proportional abundance. The concept of individual-specific core sinus microbiota, durable over time and medical therapy, but fluctuating in proportional abundance, has implications for understanding the role of bacteria in CRS pathogenesis.

Preoperative skin cultures are predictive of Propionibacterium load in deep cultures obtained at revision shoulder arthroplasty.

BACKGROUND: Propionibacterium-specific cultures are commonly positive in revised shoulders without obvious signs of infection. To help identify patients at risk for these "stealth" presentations of positive Propionibacterium cultures, we assessed the value of a preoperative skin culture in predicting the results of deep cultures obtained at the time of revision shoulder arthroplasty in patients without clinical evidence of infection. METHODS: The study enrolled 60 patients undergoing revision for a prior shoulder arthroplasty without clinical evidence of infection. A preoperative culture of the skin surface was taken before skin preparation. At surgery, multiple (mean 5.9 ± standard deviation 1.6) deep tissue and explant cultures were harvested from the shoulder. Each culture was semiquantitatively reported as the specimen Propionibacterium value (SpPV). All SpPVs from the deep specimens from each patient were summed as the total shoulder Propionibacterium score (ShPS). The averaged ShPS was the total ShPS divided by the number of deep specimens harvested. RESULTS: A multivariate analysis demonstrated that the preoperative skin SpPV was predictive of the Propionibacterium load in the revised shoulders as indicated by the total ShPS (P = .004) and averaged ShPS (P = .003). CONCLUSIONS: In this series of patients, a preoperative culture of the unprepared skin was strongly predictive of the Propionibacterium load in revised shoulder arthroplasties without clinical evidence of infection. This result suggests that the results of skin cultures taken before revision surgery may help inform operative management with respect to the need for prosthesis exchange and extended postoperative antibiotic treatment.

Temperature drives the assembly of endophytic communities' seasonal succession.

Endophytic microorganisms asymptomatically colonise plant tissues. Exploring the assembly dynamics of bacterial endophytic communities is essential to understand the functioning of the plant holobiont and to optimise their possible use as biopesticides or plant biostimulants. The variation in endophytic communities in above and below-ground organs in Vitis vinifera in the field were studied. To understand the specific effect of temperature on endophytic communities, a separate experiment was set up where grapevine cuttings were grown under controlled conditions at three different temperatures. The findings revealed the succession of endophytic communities over the year. Endophytic communities of roots and stems differ in terms of composition and dynamic response to temperature. Noticeably, compositional differences during the seasons affected bacterial taxa more in stems than in roots, suggesting that roots offer a more stable and less easily perturbed environment. Correlation abundance networks showed that the presence of several taxa (including Bradyrhizobium, Burkholderia, Dyella, Mesorhizobium, Propionibacterium and Ralstonia) is linked in both the field and the greenhouse.

Selective persistence of Propionibacterium species FMA5 following sealing of infected dentinal matrix.

The objective of the present study was to test the hypothesis that nutrient deprivation by effective isolation should inactivate causative saccharolytic bacteria occupying carious lesions. Vital maxillary third molar teeth were prepared by removing only the superficial necrotic material, leaving behind infected dentinal matrix, before the cavity was sealed with glass ionomer cement (GIC). Before sealing, lesions were biopsied to provide reference bacterial DNA for microbial analysis. After an interval of 10-12 months, the teeth were extracted and, after careful removal of GIC restoration, the underlying dentine was biopsied again for post-treatment microbial analysis. Microbial diversity for nine taxa in 45 carious lesions, before and after minimal intervention therapy, was quantified by real-time polymerase chain reaction (PCR). Except for Propionibacterium sp. FMA5, Fusobacterium nucleatum and Pseudoramibacter alactolyticus, representation of all other taxa showed reduction in the post-restoration biopsy samples. However, Propionibacterium sp. FMA5 was the only species predominantly detected in 80% of the pre-intervention, 82% of the post-restoration and 73% of the paired pre- and post-restoration biopsy samples. The median bacterial load for Propionibacterium sp. FMA5, lactobacilli and bacteria from the family Coriobacteriaceae was higher than the median bacterial load for the remaining six taxa. Significant reduction in the median bacterial load for lactobacilli was evident in post-restoration biopsy samples, implying effective control by GIC after minimal intervention. However, the median bacterial load for Propionibacterium sp. FMA5 increased in post-restoration biopsy samples. Incorporation of antimicrobial agents effective against Propionibacterium species FMA5 could add to more effective conservative management of advanced carious lesions.

Clinical characteristics and antimicrobial susceptibilities of anaerobic bacteremia in an acute care hospital.

This study investigated the clinical features of anaerobic bacteraemia in an acute-care hospital, and evaluated the antimicrobial susceptibility of these isolates to commonly available antibiotics. Microbiological and epidemiological data from 2009 to 2011were extracted from the laboratory information system and electronic medical records. One hundred and eleven unique patient episodes consisting of 116 anaerobic isolates were selected for clinical review and antibiotic susceptibility testing. Susceptibilities to amoxicillin-clavulanate, clindamycin, imipenem, metronidazole, moxifloxacin, penicillin and piperacillin-tazobactam were performed using Etest strips with categorical interpretations according to current CLSI breakpoints. Metronidazole-resistant and carbapenem-resistant anaerobic Gram-negative bacilli were screened for the nim and cfiA genes. Clinical data was obtained retrospectively from electronic medical records. During the 3 year period, Bacteroides fragilis group (41%), Clostridium species (14%), Propionibacterium species (9%) and Fusobacterium species (6%) were the most commonly isolated anaerobes. Patients with anaerobic bacteraemia that were included in the study were predominantly above 60 years of age, with community-acquired infections. The most commonly used empiric antibiotic therapies were beta-lactam/beta-lactamase inhibitor combinations (44%) and metronidazole (10%). The crude mortality was 25%, and appropriate initial antibiotic therapy was not significantly associated with improved survival. Intra-abdominal infections (39%) and soft-tissue infections (33%) accounted for nearly three-quarters of all bacteraemia. Antibiotics with the best anaerobic activity were imipenem, piperacillin-tazobactam, amoxicillin-clavulanate and metronidazole, with in-vitro susceptibility rates of 95%, 95%, 94% and 92% respectively. Susceptibilities to penicillin (31%), clindamycin (60%) and moxifloxacin (84%) were more variable. Two multidrug-resistant isolates of Bacteroides species were positive for nim and cfiA genes respectively, while another two imipenem-resistant Fusobacterium species were negative for cfiA genes. This study demonstrated that anaerobic bacteraemia in our patient population was predominantly associated with intra-abdominal and soft-tissue infections. Overall antibiotic resistance was high for penicillin and clindamycin, and the presence of emerging resistance to carbapenems and metronidazole warrants further monitoring.

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).

The microbiome of diabetic foot osteomyelitis.

The purpose of this investigation was to evaluate the diversity of bacteria in diabetic foot osteomyelitis using a 16S rRNA sequencing approach and to compare the results with conventional culture techniques. In this prospective observational study, we obtained 34 bone samples from patients admitted to our hospital with a moderate-severe diabetic foot infection. We analysed the distribution of the 16S rRNA gene sequences in the bone samples, using an Illumina MiSeq Personal Sequencer. We compared the genera that were detected with the cultured pathogens in the bone samples with conventional techniques. In the 23 samples that had positive results with both techniques, Staphylococcus, Corynebacterium, Streptococcus and Propionibacterium spp. were detected in 20, 18, 13 and 11 samples, respectively. Significantly more anaerobes were detected with 16S rRNA sequencing compared to conventional techniques (86.9 % vs. 23.1 %, p = 0.001) and more Gram-positive bacilli were present (78.3 % vs. 3.8 %, p < 0.001). Staphylococcus spp. were identified in all of the sequenced bone samples that were negative with conventional techniques. Mixed genera were present in 83.3 % (5 of 6) of the negative samples. Anaerobic and fastidious organisms may play a more significant role in osteomyelitis than previously reported. Further studies with larger populations are needed in order to fully understand the clinical importance of the microbial diversity of diabetic foot osteomyelitis.