Septic shock caused by Capnocytophaga canis after a cat scratch

Capnocytophaga canis is an uncommon cause of septic shock. Only three cases have been previously reported in the literature. In this article, we describe the case of a 70-year-old male admitted to the intensive care unit for septic shock of unknown origin. On day 2, one anaerobic bottle out of the two sets taken at admission turned positive with Gram-negative bacilli. The pathogen was identified by 16S rRNA gene as C. canis. The strain was characterized and compared with other clinical isolates of Capnocytophaga spp

Analysis of the salivary microbiome using culture-independent techniques

The salivary microbiota is a potential diagnostic indicator of several diseases. Culture-independent techniques are required to study the salivary microbial community since many of its members have not been cultivated

Analysis of the salivary microbiome using culture-independent techniques

The salivary microbiota is a potential diagnostic indicator of several diseases. Culture-independent techniques are required to study the salivary microbial community since many of its members have not been cultivated

Root Microbiota in Primary and Secondary Apical Periodontitis

Apical periodontitis is an inflammatory disease of the dental periradicular tissues triggered by bacteria colonizing necrotic root canals. Primary apical periodontitis results from the microbial colonization of necrotic pulp tissues. Secondary apical periodontitis results from a persistent infection of incorrectly treated root canals. The aim of this study was to characterize the microbiota present in primary and secondary intraradicular infections associated with apical periodontitis using 16S rRNA gene amplicon sequencing. Teeth exhibiting apical periodontitis with or without root canal treatment were extracted after informed consent. From each tooth, the intraradicular content as well as a dentin sample (control) were collected and subjected to DNA extraction. PCR amplicons of the V3–V4 region of the bacterial 16S rRNA gene were pooled and sequenced (2 × 300) on an Illumina MiSeq instrument. The bioinformatics analysis pipeline included quality filtering, merging of forward and reverse reads, clustering of reads into operational taxonomic units (OTUs), removal of putative contaminant OTUs and assigning taxonomy. The most prevalent and abundant OTU in both dentin and root canal samples was assigned to anaerobic bacterium Fusobacterium nucleatum. Multivariate analysis showed clustering of microbiota by sample type (dentin vs. intraradicular content) and, in root canals, by pathology (primary vs. secondary infection). The proportions of Enterococcus faecalis and F. nucleatum were, respectively, higher and lower when comparing secondary to primary infected root canals. Co-occurrence network analysis provided evidence of microbial interactions specific to the infection type. The identification of bacterial taxa differentially abundant in primary and secondary intraradicular infections may provide the basis for targeted therapeutic approaches aimed at reducing the incidence of apical periodontitis

Microbial Communities of Conducting and Respiratory Zones of Lung-Transplanted Patients.

Background: Lung transplantation (LT) is a recognized treatment for end-stage pulmonary disease. Bacteria from the recipient nasopharynx seed the new lungs leading to infections and allograft damage. Understanding the characteristics and topological variations of the microbiota may be important to apprehend the pathophysiology of allograft dysfunction. Objectives: To examine the characteristics and relationship of bacterial compositions between conducting and respiratory zones of the allograft. Methods: We performed 16S rRNA gene sequencing on bronchial aspirates (BAs) and bronchoalveolar lavages (BALs) collected in pairs in 19 patients at several time-points post-LT. Results: The respiratory zone was characterized independently of the time post-LT by a higher bacterial richness than the conducting zone (p = 0.041). The phyla Firmicutes and Proteobacteria dominated both sampling zones, with an inverse correlation between these two phyla (Spearman r = -0.830). Samples of the same pair, as well as pairs from the same individual clustered together (Pseudo-F = 3.8652, p < 0.01). Microbiota of BA and BAL were more closely related in samples from the same patient than each sample type across different patients, with variation in community structure being mainly inter-individual (p < 0.01). Both number of antibiotics administered (p < 0.01) and time interval post-LT (p < 0.01) contributed to the variation in global microbiota structure. Longitudinal analysis of BA-BAL pairs of two patients showed dynamic wave like fluctuations of the microbiota. Conclusions: Our results show that post-transplant respiratory zones harbor higher bacterial richness, but overall similar bacterial profiles as compared to conductive zones. They further support an individual microbial signature following LT

Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR

Identification of unexpected taxa in 16S rRNA surveys of low-density microbiota, diluted mock communities and cultures demonstrated that a variable fraction of sequence reads originated from exogenous DNA. The sources of these contaminants are reagents used in DNA extraction, PCR, and next-generation sequencing library preparation, and human (skin, oral and respiratory) microbiota from the investigators

Mycoplasma genitalium Endocarditis in Prosthetic Aortic Valve

We report a case of Mycoplasma genitalium endocarditis in a prosthetic heart valve of a woman who sought care in Switzerland for acute aortic valve dysfunction 3 years after valve replacement. This unusual manifestation of infection with this bacterium was diagnosed using broad-range PCR despite suspicion of a mechanical disinsertion

Rare Case of Community-Acquired Endocarditis Caused by Neisseria meningitidis Assessed by Clinical Metagenomics.

The most common causes of infective endocarditis (IE) are Staphylococcus, Streptococcus, Enterococcus, and HACEK-related organisms. In 15-30% of the IE cases, standard blood cultures remain sterile. We aimed at identifying the causative agent of a blood-culture-negative IE by whole metagenome shotgun sequencing (WMGS). A 54-year old woman diagnosed with community-onset pneumonia by a general practitioner, was admitted with dyspnea, cough and fever. The patient's blood cultures were repeatedly negative. The transesophageal echocardiography and transthoracic echocardiography showed an echo density on the left coronary leaflet of the aortic valve and signs suggestive of a ruptured abscess of the mitro-aortic junction. The patient underwent a semi-urgent aortic valve replacement by a mechanical prosthetic valve. We extracted DNA from the surgically-removed fresh valve tissue. The extraction procedure included bacterial/fungal DNA enrichment procedure. Nextera XT library prepared from the valve DNA extract was sequenced (2 × 250) on an Illumina MiSeq instrument. Sequence reads were mapped against bacterial genomic sequences, 16S rRNA genes and clade-specific taxonomic markers. Most of the 103,136 sequencing reads classified as bacterial were assigned to Neisseria meningitidis. In line with these data, mapping of reads against clade-specific and 16S rRNA gene markers revealed N. meningitidis as the most represented species. Assembled metagenomic fragments had the best average nucleotide identity (ANI) with N. meningitidis. Comparison of assembled contigs to reference alleles showed that this strain belongs to the ST-41/44 complex. N. meningitidis is commonly associated with meningitis and/or septicemia but should not be neglected as a causative agent of IE, which became exceedingly rare with the introduction of antibiotics. Our data show that WMGS may be used as a diagnostic procedure to strengthen the diagnosis of IE and to obtain draft genomic sequence of the pathogen and typing information

Additional file 2: Figure S2. of Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR

Effect of in silico decontamination on taxonomic profiles of culture dilutions and negative extraction controls. Means for three samples obtained in separate DNA extraction experiments are given. The R-OTU (ratio between mean ‘absolute’ abundance of OTUs in negative extraction controls and culture samples) cut-offs of 1 to 0.001 were applied for decontamination. This ratio was calculated from the relative OTU abundance and qPCR data obtained using the E. coli standard curve. Dilutions of the master stock are indicated from 1E0 (no dilution) to 1E-8 (10−8). EC, E. coli; SA, S. aureus. NEC_W, negative extraction controls obtained by substituting culture for water; NEC_B, negative extraction controls obtained by substituting culture for lysis buffer; ND, no decontamination was performed. (PDF 16 kb

Additional file 1: Figure S1. of Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR

Relative abundance of bacterial genera before and after the decontamination procedure. Genera with mean relative abundance >0.5 % in negative extraction controls are presented. The proportion is indicated by the scale at the bottom of the plot. The R-OTU (ratio between mean ‘absolute’ abundance of OTUs in negative extraction controls and culture samples) cut-off of 0.01 was applied for decontamination. This ratio was calculated from the relative OTU abundance and qPCR data obtained using the S. aureus standard curve. For a given culture/dilution or negative extraction control, the data obtained from DNA extractions performed at three different time points (Exp1–Exp3) are presented from left to right. Dilutions of the master stock are indicated from 1E0 (no dilution) to 1E-8 (10−8). NEC_W, negative extraction controls obtained by substituting culture for water; NEC_B, negative extraction controls obtained by substituting culture for lysis buffer. (PDF 13 kb