Eggerthella lenta bacteremia complicated by spondylodiscitis, psoas abscess, and meningitis

First periprosthetic hip infection caused by Eggerthella lenta

Periprosthetic joint infection (PJI) caused by anaerobic, Gram-positive bacilli is rare. We present here a case of an 83-year-old female patient who was admitted to our tertiary referral arthroplasty center to treat a complex PJI of her right hip joint after multiple failed surgeries. External and intraoperative cultures reveald growth of Eggerthella lenta (E. lenta). Microbiological identification was fast but in a very few samples. A successful management, comprising of radical debridement with one-stage exchange and an antibiotic treatment with multiple antibiotics, has been achieved at 24-month follow-up. To the best of our knowledge, we have provided the first case study of a hip PJI caused by E. lenta successfully treated with one-stage exchange and an adequate antibiotic treatment.

Eggerthella lenta bacteremia successfully treated with ceftizoxime: case report and review of the literature

Eggerthella lenta is a normal human microflora that is anaerobic, non-sporulating, and Gram positive. However, an increasing number of studies have shown that it could also be an important pathogen for humans, even causing life-threatening infection under certain conditions. However, understanding its pathogenic mechanism and treatment options still need to be improved; more clinical data are needed to explore it further. In this article, we report a case of ceftizoxime-cured E. lenta bacteremia and review the recent literature to provide more clinical data for the diagnosis of E. lenta bacteremia. Our report suggests that the frequency of E. lenta bacteremia is increased in patients with hematologic or solid organ cancer, diabetes mellitus and also in those with appendicitis.

Vertebral osteomyelitis in bacterial meningitis patients

OBJECTIVE

To analyze the clinical and laboratory characteristics of vertebral osteomyelitis in community-acquired bacterial meningitis patients.

METHODS

All episodes of vertebral osteomyelitis in a cohort study of adult patients with community-acquired bacterial meningitis in the Netherlands were analyzed. Subsequently, a systematic review of published cases was performed.

RESULTS

Between March 2006 and August 2018, 10 of 1974 (0.5%) meningitis patients were diagnosed with vertebral osteomyelitis. The median age was 70 years (interquartile range (IQR) 54-74 years); six (60%) were male and four (40%) were female. The median time between diagnosis of bacterial meningitis and vertebral osteomyelitis was 6 days (IQR 1-13 days). The most common presenting symptoms were back or neck pain, occurring in seven patients (70%); one patient presented with neurological deficits due to cauda equina compression. Streptococcus pneumoniae was the causative pathogen in five patients and Staphylococcus aureus in three. The literature review identified 32 additional cases, showing a similar distribution by age, sex, and pathogen. Seven (18%) of 40 patients from the series presented here and those reported in the literature died.

CONCLUSIONS

Concomitant vertebral osteomyelitis is rare in community-acquired bacterial meningitis patients. Persisting back pain is a clue to the diagnosis and should prompt magnetic resonance imaging of the spine, because prolonged antibiotic treatment or surgical treatment may be indicated.

Eggerthella lenta Bacteremia in a Middle-Aged Healthy Man with Acute Hepatic Abscess: Case Report and Literature Review, 1970-2020

Eggerthella lenta (E. lenta) is a rare but significant human emerging pathogen. Infections caused by it are rare and little-known, both on clinical and therapeutical aspects, in spite of new emergence of bacteria isolation and identification techniques. In this article, we report a case involving a previously healthy 52-year-old man suffering from a newly diagnosed hepatic abscess who developed E. lenta bacteremia, which was treated successfully using empirical therapy with ertapenem and teicoplanin. To the best of our knowledge, this is the first documented report of E. lenta bacteremia related specifically to liver abscess. Cases related to this bacterial species are infrequent and sporadic; thus, we reviewed English literature on E. lenta infection in PubMed/MEDLINE in the last 50 years. A total of 31 sporadic cases were identified. The majority of patients were male (71%), had an average age of 54.3 years and presented predisposing conditions, such as digestive system trouble (45.2%), immunocompromised state (25.8%) or risk factors (22.6%). Two of the cases had more than one predisposing factors. Fever was common (93.5%). Average days to diagnosis of them were 6.8 days. MALDI-TOF MS is emerging as a fast and useful tool in the identification of it. Teicoplanin, vancomycin, amoxicillin-clavulanate, metronidazole, clindamycin, cefoxitin, chloramphenicol, and carbapenems appear to be the most used antibiotic treatment options. The purpose of this review is to increase awareness about the clinical infections caused by E. lenta.

Permutation-based identification of important biomarkers for complex diseases via machine learning models

Study of human disease remains challenging due to convoluted disease etiologies and complex molecular mechanisms at genetic, genomic, and proteomic levels. Many machine learning-based methods have been developed and widely used to alleviate some analytic challenges in complex human disease studies. While enjoying the modeling flexibility and robustness, these model frameworks suffer from non-transparency and difficulty in interpreting each individual feature due to their sophisticated algorithms. However, identifying important biomarkers is a critical pursuit towards assisting researchers to establish novel hypotheses regarding prevention, diagnosis and treatment of complex human diseases. Herein, we propose a Permutation-based Feature Importance Test (PermFIT) for estimating and testing the feature importance, and for assisting interpretation of individual feature in complex frameworks, including deep neural networks, random forests, and support vector machines. PermFIT (available at https://github.com/SkadiEye/deepTL) is implemented in a computationally efficient manner, without model refitting. We conduct extensive numerical studies under various scenarios, and show that PermFIT not only yields valid statistical inference, but also improves the prediction accuracy of machine learning models. With the application to the Cancer Genome Atlas kidney tumor data and the HITChip atlas data, PermFIT demonstrates its practical usage in identifying important biomarkers and boosting model prediction performance.

Study of human disease remains challenging due to convoluted disease etiologies and complex molecular mechanisms at genetic, genomic, and proteomic levels. Here, the authors propose a computationally efficient Permutation-based Feature Importance Test to assist interpretation and selection of individual features in complex machine learning models for complex disease analysis.

A rare case of non-clostridial infection in a non-diabetic patient

A 76-year-old man presented with neck swelling associated with pain and fever. On examination, there was a submental neck swelling. His initial CT scan showed multiloculated abscess centred in the left submandibular gland. He remained febrile despite on intravenous ceftriaxone and metronidazole. A repeat CT scan revealed significant worsening with multiple pockets of fluids with gas locules in the deep neck spaces. He subsequently underwent neck exploration and drainage of neck abscess. Extensive necrotic tissue was found intraoperatively and thick pus was drained from the bilateral parapharyngeal, submental spaces and anterior mediastium. Pus culture profusely grew of Eggerthella species. Patient recovered well following further intravenous antibiotic therapy. Diabetes mellitus and odontogenic infections are the common risk factors in deep neck infections. Our patient is however non-diabetic and edentulous. Current case is presented to serve as a rare case of neck abscess with unusual cause in a non-diabetic patient.

Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut

As part of the culturomics project aiming at describing the human microbiota, we report in this study the description of the new bacterial genus Raoultibacter gen. nov. that includes two new species, that is, R. massiliensis sp. nov. and R. timonensis sp. nov. The R. massiliensis type strain Marseille-P2849T was isolated from the fecal specimen of a healthy 19-year-old Saudi Bedouin, while R. timonensis type strain Marseille-P3277T was isolated from the feces of an 11-year-old pygmy female living in Congo. Strain Marseille-P2849T exhibited 91.4% 16S rRNA sequence similarity with Gordonibacter urolithinfaciens, its phylogenetic closest neighbor with standing in nomenclature. As well, strain Marseille-P3277T exhibited 97.96% 16S rRNA similarity with strain Marseille-P2849T . Both strains were Gram-positive, motile, nonspore-forming rod and form transparent microcolonies on blood agar in both anaerobic and microaerophilic atmospheres. The genome sizes of strain Marseille-P2849T and strain Marseille-P3277T were 3,657,161 bp and 4,000,215 bp, respectively. Using a taxono-genomic approach combining the phenotypic, biochemical, and genomic characteristics, we propose the genus Raoultibacter gen. nov., which contains strains Marseille-P2849T (= CSUR P2849T , = DSM 103407T ) and Marseille-P3277T (=CCUG 70680T , =CSUR P3277T ) as type strains of the species R. massiliensis sp. nov., and R. timonensis sp. nov., respectively.

Postpartum endometritis and obstetrical sepsis associated with Eggerthella lenta. Case report and review of the literature

Sepsis, associated with Eggerthella lenta is rarely reported, despite current possibilities for microorganisms isolation and identification. About 100 cases of bacteriemia associated with this pathogen have been reported so far. Postpartum infectious complications are mostly associated with bacterial inhabitants of gastrointestinal tract and vagina, including obligatory anaerobes. This case report highlights E. lenta-associated severe endometritis complicated by abdominal sepsis in a young healthy woman, and the challenges of antibacterial therapy.

Phoenicibacter congonensis gen. nov., sp. nov., a new genus isolated from the human gut and its description using a taxonogenomic approach

Culturomics has recently allowed the isolation and description of previously uncultured bacteria from the human microbiome at different body sites. As part of a project aiming to describe the human gut microbiota by culturomics, Phoenicibacter congonensis strain Marseille-P3241^T was isolated from the gut of a 45 years old Pygmy female. In the present work, we aim to describe this strain via the taxonogenomics approach. The major phenotypic, genomic and biochemical characteristics of this strain were analysed. Strain Marseille-P3241^T is an anaerobic, Gram-positive and motile coccobacillus that grows optimally at 37 °C. The genome of strain Marseille-P3241^T is 1,447,956 bp long with 43.44% GC content and its 16S rRNA gene sequence exhibited 89% sequence similarity with that of Denitrobacterium detoxificans strain NPOH1^T, the phylogenetically closest related species with current standing in nomenclature. After performing a phylogenetic and genomic analysis, we conclude that strain Marseille-P3241^T (= CCUG 70681^T = CSUR P3241^T) represents the type species of a new genus, for which we propose the name Phoenicibacter congonensis gen. nov., sp. nov.

Lack of Vitamin D Receptor Causes Dysbiosis and Changes the Functions of the Murine Intestinal Microbiome

PURPOSE

The microbiome modulates numerous aspects of human physiology and is a crucial factor in the development of various human diseases. Vitamin D deficiency and downregulation of the vitamin D receptor (VDR) are also associated with the pathogenesis of diseases such as inflammatory bowel disease, cancers, obesity, diabetes, and asthma. VDR is a nuclear receptor that regulates the expression of antimicrobial peptides and autophagy regulator ATG16L1. Vitamin D may promote a balanced intestinal microbiome and improve glucose homeostasis in diabetes. However, how VDR regulates microbiome is not well known. In the current study, we hypothesize that VDR status regulates the composition and functions of the intestinal bacterial community.

METHODS

Fecal and cecal stool samples were harvested from Vdr knockout (Vdr(-/-)) and wild-type mice for bacterial DNA and then sequenced with 454 pyrosequencing. The sequences were denoised and clustered into operational taxonomic units, then queried against the National Center for Biotechnology Information database. Metagenomics were analyzed, and the abundances of genes involved in metabolic pathways were compared by reference to the Kyoto Encyclopedia of Genes and Genomes and Clusters of Orthologous Groups databases.

FINDINGS

In the Vdr(-/-) mice, Lactobacillus was depleted in the fecal stool, whereas Clostridium and Bacteroides were enriched. Bacterial taxa along the Sphingobacteria-to-Sphingobacteriaceae lineage were enriched, but no genera reached statistical significance. In the cecal stool, Alistipes and Odoribacter were depleted, and Eggerthella was enriched. Notably, all of the taxa upstream of Eggerthella remained unchanged. A comparison of Vdr(-/-) and wild-type samples revealed 40 (26 enriched, 14 depleted) and 72 (41 enriched, 31 depleted) functional modules that were significantly altered in the cecal and fecal microbiomes, respectively (both, P < 0.05), due to the loss of Vdr. In addition to phylogenetic differences in gut microbiome with different intestinal origins, we identify several important pathways, such as nucleotide-binding oligomerization domain-like receptor, affected by Vdr status, including amino acid, carbohydrate, and fatty acid synthesis and metabolism, detoxification, infections, signal transduction, and cancer and other diseases.

IMPLICATIONS

Our study fills knowledge gaps by having investigated the microbial profile affected by VDR. Insights from our findings can be exploited to develop novel strategies to treat or prevent various diseases by restoring VDR function and healthy microbe-host interactions.

Clinical and microbiological characteristics of Eggerthella lenta bacteremia

Eggerthella lenta is an emerging pathogen that has been underrecognized due to historical difficulties with phenotypic identification. Until now, its pathogenicity, antimicrobial susceptibility profile, and optimal treatment have been poorly characterized. In this article, we report the largest cohort of patients with E. lenta bacteremia to date and describe in detail their clinical features, microbiologic characteristics, treatment, and outcomes. We identified 33 patients; the median age was 68 years, and there was no gender predominance. Twenty-seven patients (82%) had serious intra-abdominal pathology, often requiring a medical procedure. Of those who received antibiotics (28/33, 85%), the median duration of treatment was 21.5 days. Mortality from all causes was 6% at 7 days, 12% at 30 days, and 33% at 1 year. Of 26 isolates available for further testing, all were identified as E. lenta by both commercially available matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems, and none were found to harbor a vanA or vanB gene. Of 23 isolates which underwent susceptibility testing, all were susceptible to amoxicillin-clavulanate, cefoxitin, metronidazole, piperacillin-tazobactam, ertapenem, and meropenem, 91% were susceptible to clindamycin, 74% were susceptible to moxifloxacin, and 39% were susceptible to penicillin.

Bacteremia caused by Eggerthella lenta in an elderly man with a gastrointestinal malignancy: A case report

Eggerthella lenta is an anaerobic, Gram-positive bacillus commonly found in the human digestive tract. Occasionally, it can cause life-threatening infections. Bacteremia due to this organism is always clinically significant and is associated with gastrointestinal diseases and states of immune suppression. The authors report a case involving an elderly man with a newly diagnosed gastrointestinal malignancy who developed bacteremia caused by E lenta, treated successfully using empirical therapy with vancomycin and piperacillin-tazobactam, followed by directed therapy with metronidazole once the identity and antibiotic susceptibility of the organism was established. The present case reinforces the connection between E lenta bacteremia with gastrointestinal malignancy and highlights the importance of searching for a source of bacteremia due to this organism.