ABSTRACT
Dielma fastidiosa is a gram-negative, anaerobic rod belonging to the family Erysipelotrichaceae. D. fastidiosa has previously been isolated in human stool samples as part of the commensal flora; however, prior to this case, it has never been identified as a human pathogen. We present the first case of bacteraemia with D. fastidiosa. Bacterial growth in the blood culture bottle was detected by the automated blood culture system BacT/ALERT 3D. Culturing was performed, and bacterial colonies were identified as D. fastidiosa using MALDI-TOF MS. A subsequent whole-genome sequencing using Illumina NovaSeq was performed, and a phylogenetic tree depicting all available sequences of D. fastidiosa was generated. The reference MALDI-TOF spectrum and species identification was compared with the previously published spectrum. Whole-genome sequencing confirmed the tentative MALDI-TOF species identification. Notably, the maximum-likelihood-based phylogenetic analysis placed the D. fastidiosa isolate from this clinical case within the known variation of the eight publicly available sequences of this species. We identified D. fastidiosa by whole-genome sequencing followed by maximum-likelihood analysis as a possible pathogen in this case of bacteraemia in a patient hospitalized with diverticulitis.
Subject(s)
Bacteremia , Diverticulitis , Humans , Phylogeny , Likelihood Functions , Bacteremia/diagnosis , Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationABSTRACT
Microorganisms play a primary role in regulating biogeochemical cycles and are a valuable source of enzymes that have biotechnological applications, such as carbohydrate-active enzymes (CAZymes). However, the inability to culture the majority of microorganisms that exist in natural ecosystems restricts access to potentially novel bacteria and beneficial CAZymes. While commonplace molecular-based culture-independent methods such as metagenomics enable researchers to study microbial communities directly from environmental samples, recent progress in long-read sequencing technologies are advancing the field. We outline key methodological stages that are required as well as describe specific protocols that are currently used for long-read metagenomic projects dedicated to CAZyme discovery.
Subject(s)
Metagenomics , Microbiota , Metagenomics/methods , Metagenome , Carbohydrates , High-Throughput Nucleotide SequencingABSTRACT
We report a coronavirus disease 2019 case with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) persisting beyond 333 days in an immunocompromised patient with chronic lymphocytic leukemia, asymptomatically carrying infectious SARS-CoV-2 at day 197 postdiagnosis. In addition, viral sequencing indicates major changes in the spike protein over time, temporally associated with convalescent plasma treatment.
