Novel fastidious, partially acid-fast, anaerobic Gram-positive bacillus associated with abscess formation and recovered from multiple medical centers

Infection caused by Lawsonella clevelandensis after breast augmentation with autologous fat grafting: a case report

BACKGROUND

Lawsonella clevelandensis is one recently documented anaerobic, which is partially acid-fast. Nevertheless, it is rarely found to be associated with human infections, especially in scope of plastic and cosmetic surgery before our patient who was performed breast augmentation with autologous fat grafting. Breast augmentation is becoming popular, the most common post-surgery complication of which is bacterial infection.

CASE PRESENTATION

A 29-year-old female who was found swelling in her right breast and fever after breast augmentation surgery with autologous fat grafting was administered. Before administration, she had been treated with antibiotics (details unknown) for more than 1 month without any significant improvements. After administration, she was treated with intravenous antibiotic empirically and repeated debridement via Vaccuum Sealing Drainage (VSD). And samples of the necrotic tissues and pus collected in surgery were sent for microbiological testing. However, routine examination failed. Thus samples were further collected and sent to Genoxor Medical & Science Technology Inc. (Shanghai, China) to conduct Next-Generation Sequencing (NGS). Surprisingly Lawsonella clevelandensis was determined. Accordingly, sensitive antibiotic was applied in concert with thorough debridement and drainage and finally her condition was completely reversed with wound closure gradually.

CONCLUSION

Complications of breast augmentation with autologous fat graft are various, of which infection is most common. Rare pathogen such as Lawsonella clevelandensis infection in human is rare in clinical practice. Moreover, it is difficult to differentiate from non-tuberculous mycobacterium for its partial acid resistance, difficulty to culture and abscess formation. How to determine diagnosis of Lawsonella clevelandensis infection accurately come to be critical In our report, NGS is recommended as a useful method to identify the pathogen, which may provide us a novel tool for refractory wound.

Lawsonella clevelandensis, a case series of vascular graft infections caused by a rare pathogen

Lawsonella clevelandensis is a fastidious Gram-positive, partially acid-fast, anaerobic, catalase positive bacterium that has been reported to be a rare cause of abdominal, breast, spinal, and liver abscesses. Here, three L. clevelandensis vascular graft infections (VGIs) and cardiac infections are reported.

Lawsonella clevelandensis is a rare cause of infected chronic contained rupture of abdominal aortic aneurysm

Lawsonella clevelandensis is an anaerobic, partially acid-fast, Gram-positive bacillus associated with abscess formation. We present the case of a 70-year-old male with chronic contained rupture of abdominal aortic aneurysm (CCR-AAA) complicated by intra-abdominal abscess formation. An abdominal computed tomography scan revealed a rim-enhancing retroperitoneal collection tracking into the subcutaneous layer of the left flank and buttock, suggestive of CCR-AAA with infected haematoma. He underwent ultrasound-guided needle aspiration of the intra-abdominal collection. Conventional culture techniques failed to isolate L. clevelandensis, and the diagnosis was only confirmed by means of 16S rRNA PCR. The patient underwent branched endovascular repair of his aneurysm, and was commenced on treatment with co-amoxiclav, resulting in significant reduction in the size of the infected collection. This is only the second reported case of infection with L. clevelandensis in the UK, and the first reported case of this organism causing infected CCR-AAA.

Lawsonella clevelandensis: an emerging cause of vascular graft infection

Lawsonella clevelandensis, an emerging pathogen, was first described in 2016, and has been implicated in abdominal, breast and spinal abscesses in a limited number of cases. Being a fastidious organism, it is primarily identified with molecular methods. With the incorporation of broad-range PCR testing in clinical diagnostics, L. clevelandensis has been increasingly reported in the literature. We describe a case of a 65-year-old man who presented with bilateral psoas abscesses secondary to aorto-bi-iliac vascular graft infection with L. clevelandensis identified using 16S rRNA/PCR sequencing. The patient underwent surgical resection and replacement of infected graft, followed by 6 weeks of intravenous antibiotic therapy and then chronic suppression with doxycycline and cefadroxil. He was infection-free at last follow-up.

Liver abscess caused by Lawsonella clevelandensis in a patient with rheumatoid arthritis: A case report and literature review

Lawsonella clevelandensis is a recently described anaerobic and partially acid-fast bacterium within the order Corynebacterineae. It is a fastidious microorganism that has been identified as part of the oral microbiota and is rarely associated with human infections. We describe the case of a 70-year-old man with a history of rheumatoid arthritis that developed liver abscesses and pylephlebitis. Gram stain of purulent material obtained by percutaneous drainage of the hepatic collection revealed gram-positive bacilli that stained acid-fast by the Kinyoun method. The patient was initially treated with imipenem, moxifloxacin and clarithromycin for possible Nocardia and/or nontuberculous mycobacterial infection. Cultures failed to grow the organism seen on the stains, and broad-spectrum 16S rRNA PCR gene sequencing analysis identified it as Lawsonella clevelandensis. Treatment was de-escalated to amoxicillin/clavulanic acid. The hepatic abscesses resolved completely after 4 weeks of treatment.

There are only 8 documented cases of human infection caused by Lawsonella clevelandensis reported in the literature. Conventional microbiological methods do not reliably detect this bacterium, and the diagnosis relies on molecular methods. Excellent outcomes are obtained with a combined treatment approach that includes abscess drainage and prolonged antibiotic therapy.

Cutaneous nocardiosis with discharging sinus clinically mimicking tuberculosis diagnosed by cytology

Nocardiosis is primarily a pulmonary infection commonly seen in immunocompromised individuals. However, lymphocutaneous nocardiosis is observed in immunocompetent individuals often after trauma. The clinical and cytomorphological features of lymphocutaneous nocardiosis closely mimic the most common infections in India such as tuberculosis and mycetoma (very common cutaneous infection with discharging sinus). As it is crucial to differentiate nocardiosis from tuberculosis, to avoid unnecessary antitubercular treatment, special stains like modified Ziehl-Neelsen stain and Gram stain can be employed to differentiate the morphology of Nocardia from tuberculosis. Fine-needle cytology from these cutaneous lesions helps in yielding adequate material for rapid and accurate diagnosis of immediate specific antibiotic treatment. We report a rare case that presented with clinical diagnosis of tuberculosis but turned out to be nocardiosis on cytomorphology with simple and most feasible fine-needle aspiration method of tissue diagnosis and scrape cytology.

ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples

Analysis of 16S ribosomal RNA (rRNA) gene amplification data for microbial barcoding can be inaccurate across complex environmental samples. A method, ANCHOR, is presented and designed for improved species‐level microbial identification using paired‐end sequences directly, multiple high‐complexity samples and multiple reference databases. A standard operating procedure (SOP) is reported alongside benchmarking against artificial, single sample and replicated mock data sets. The method is then directly tested using a real‐world data set from surface swabs of the International Space Station (ISS). Simple mock community analysis identified 100% of the expected species and 99% of expected gene copy variants (100% identical). A replicated mock community revealed similar or better numbers of expected species than MetaAmp, DADA2, Mothur and QIIME1. Analysis of the ISS microbiome identified 714 putative unique species/strains and differential abundance analysis distinguished significant differences between the Destiny module (U.S. laboratory) and Harmony module (sleeping quarters). Harmony was remarkably dominated by human gastrointestinal tract bacteria, similar to enclosed environments on earth; however, Destiny module bacteria also derived from nonhuman microbiome carriers present on the ISS, the laboratory's research animals. ANCHOR can help substantially improve sequence resolution of 16S rRNA gene amplification data within biologically replicated environmental experiments and integrated multidatabase annotation enhances interpretation of complex, nonreference microbiomes.

An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017

Recognition and acknowledgment of novel bacterial taxonomy and nomenclature revisions can impact clinical practice, disease epidemiology, and routine clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM) herein presents its biannual report summarizing such changes published in the years 2016 and 2017, as published and added by the International Journal of Systematic and Evolutionary Microbiology Noteworthy discussion centers around descriptions of novel Corynebacteriaceae and an anaerobic mycolic acid-producing bacterium in the suborder Corynebacterineae; revisions within the Propionibacterium, Clostridium, Borrelia, and Enterobacter genera; and a major reorganization of the family Enterobacteriaceae. JCM intends to sustain this series of reports as advancements in molecular genetics, whole-genome sequencing, and studies of the human microbiome continue to produce novel taxa and clearer understandings of bacterial relatedness.

Lawsonella clevelandensis causing spinal subdural empyema

Lawsonella clevelandensis is a recently described species and genus of bacterium in the Corynebacterineae suborder which is Gram-stain positive, partially acid-fast and anaerobic. Very few cases of human infection due to this organism are described and here we seek to add to the limited medical literature. We report the case of a 2-year-old girl who presented with an infected spinal dermoid cyst secondary to Lawsonella clevelandensis which required surgical drainage and a long course of antibiotics. We encountered diagnostic and therapeutic difficulties because this is a fastidious organism which was difficult to culture and ultimately required molecular detection and identification. To the best of our knowledge, this is only the seventh reported case of Lawsonella clevelandensis causing human infection worldwide and the first in the UK. This is the first reported case of Lawsonella clevelandensis infection in a child and the second reported case of this organism causing spinal infection.

New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract

The expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most next-generation sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus, and mouth. Using minimum entropy decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level, revealing four key insights. First, we discovered that Lawsonella clevelandensis, a recently named bacterium, and Neisseriaceae [G-1] HMT-174, a previously unrecognized bacterium, are common in adult nostrils. Second, just 19 species accounted for 90% of the total sequences from all participants. Third, 1 of these 19 species belonged to a currently uncultivated genus. Fourth, for 94% of the participants, 2 to 10 species constituted 90% of their sequences, indicating that the nostril microbiome may be represented by limited consortia. These insights highlight the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function. Also, in this cohort, three common nasal species (Dolosigranulum pigrum and two Corynebacterium species) showed positive differential abundance when the pathobiont Staphylococcus aureus was absent, generating hypotheses regarding colonization resistance. By facilitating species-level taxonomic assignment to microbes from the human aerodigestive tract, the eHOMD is a vital resource enhancing clinical relevance of microbiome studies. IMPORTANCE The eHOMD (http://www.ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes and the individual microbes in body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus, and mouth, and the lower respiratory tract, in health and disease. The eHOMD is an actively curated, web-based, open-access resource. eHOMD provides the following: (i) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (ii) a systematic naming scheme for unnamed and/or uncultivated microbial taxa, (iii) reference genomes to facilitate metagenomic, metatranscriptomic, and proteomic studies and (iv) convenient cross-links to other databases (e.g., PubMed and Entrez). By facilitating the assignment of species names to sequences, the eHOMD is a vital resource for enhancing the clinical relevance of 16S rRNA gene-based microbiome studies, as well as metagenomic studies.

Lawsonella clevelandensis as the causative agent of a breast abscess

Lawsonella clevelandensis is a Gram-stain-positive, partially acid-fast, anaerobic, being considered a new species within a new genus in the suborder Corynebacterineae. There are only a few cases reported worldwide. This is a fastidious microorganism, difficult to identify by conventional methods, leading to inappropriate treatments. The authors report a case of a 29-year-old woman with a 3-week evolution of a breast nodule. There was a family history of breast carcinoma. Samples were collected for histological and microbiological examination. Gram staining revealed Gram-positive filamentous bacilli, acid-fast-positive. The cultural examination revealed a Lawsonella clevelandensis that was confirmed by molecular methods. At the last follow up, the evolution was favorable; the abscess was resolved, with no evidence of recurrence. To our knowledge the present case was the first reported in Europe.

Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2016

A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate identification and rapid reporting and communication to medical staff regarding patients with infectious agents of clinical importance. Microbial taxonomy in the age of molecular diagnostics and phylogenetics creates changes in taxonomy at a logarithmic rate further complicating this process. This update focuses on the description of new species and classification changes proposed in 2016.

Can anaerobes be acid fast? A novel, clinically relevant acid fast anaerobe

INTRODUCTION

Anaerobic acid fast bacilli (AFB) have not been previously reported in clinical microbiology. This is the second case report of a novel anaerobic AFB causing disease in humans.

CASE PRESENTATION

An anaerobic AFB was isolated from an abdominal wall abscess in a 64-year-old Caucasian diabetic male, who underwent distal pancreatectomy and splenectomy for resection of a pancreatic neuroendocrine tumour. The isolated bacteria were gram-variable and acid-fast, consisting of small irregular rods. The 16S rRNA gene sequence analysis showed that the isolate is a novel organism described in the literature only once before. The organism was studied at the CDC (Centers for Disease Control and Prevention) by the same group that worked with the isolates from the previous report; their findings suggest that the strain belongs to the suborder Corynebacterineae.

CONCLUSION

This is the fifth reported case of an anaerobic AFB involved in clinical disease; its microbiological features and 16S RNA sequence are identical to previously reported cases. Clinical disease with this organism seems to be associated with recent history of surgery and abscess formation in deep soft tissues. Acquisition from surgical material is uncertain but seems unlikely.

Lawsonella clevelandensis gen. nov., sp. nov., a new member of the suborder Corynebacterineae isolated from human abscesses

Gram-stain-positive, partially acid-fast, non-spore-forming, anaerobic, catalase-positive, pleomorphic bacteria were isolated from human abscesses. Strains X1036T, X1698 and NML 120705, were recovered from a spinal abscess, a peritoneal abscess and a breast abscess respectively. A phylogenetic analysis of the 16S rRNA gene sequences showed that the strains shared 100 % similarity, and the nearest phylogenetic neighbour was Dietzia timorensis DSM 45568T (95%). Chemotaxonomic characteristics of the strains were consistent with those described for members of the suborder Corynebacterineae. Mycolic acids were detected using HPLC and one-dimensional TLC; whole-cell hydrolysates yielded meso-diaminopimelic acid with arabinose and galactose as the predominant sugars; the muramic acid acyl type was acetylated; the major menaquinone was MK-9 (96.3%); polar lipids detected were phosphatidylglycerol, phosphatidylinositol and an unknown glycophospholipid. Cellular fatty acids were hexadecanoic acid (C16 : 0), octadecenoic acid (C18 : 1ω9c) and decanoic acid (C10 : 0). Tuberculostearic acid was not detected. Based on the results of this polyphasic study, we conclude that these strains represent a novel genus and species within the suborder Corynebacterineae for which we propose the name Lawsonella clevelandensis gen. nov., sp. nov., with the type strain X1036T (=DSM 45743T=CCUG 66657T).

Complete Genome Sequences for Two Strains of a Novel Fastidious, Partially Acid-Fast, Gram-Positive Corynebacterineae Bacterium, Derived from Human Clinical Samples

Here we report the complete genome sequences of two strains of the novel fastidious, partially acid-fast, Gram-positive bacillus "Lawsonella clevelandensis" (proposed). Their clinical relevance and unusual growth characteristics make them intriguing candidates for whole-genome sequencing.