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Long S, Tang P, Ouyang P, Liao X, Xie L. A Case Report of a Rare Pulmonary Opportunistic Infection in an Infant Caused by Tsukamurella tyrosinosolvens. Int Med Case Rep J 2024; 17:725-731. [PMID: 39100685 PMCID: PMC11298180 DOI: 10.2147/imcrj.s471682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/20/2024] [Indexed: 08/06/2024] Open
Abstract
This case report describes the case of a female infant hospitalized for severe pneumonia. During the treatment process, various antibiotics are used to treat and prevent further infection. The child had a weak physical condition, combined with neuroblastoma, paraneoplastic syndrome, and low immune function, leading to Tsukamurella tyrosinosolvens infection. The treatment was eventually abandoned owing to poor prognosis. This study aims to through the medium, dyeing, electron microscope observation, 16s rRNA and high-throughput sequencing investigated the morphological characteristics, staining properties, electron microscope morphology, antibiotic resistance, and genomic characteristics of Tsukamurella tyrosinosolvens. The aim of the study is to provide data reference for clinical laboratory staff in bacteria identification research, and to provide relevant help for clinicians in diagnosis and treatment.
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Affiliation(s)
- Sheng Long
- Department of Clinical Laboratory, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People’s Republic of China
| | - Peijuan Tang
- Department of Clinical Laboratory, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People’s Republic of China
| | - Pengwen Ouyang
- Department of Clinical Laboratory, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People’s Republic of China
| | - Xiangjian Liao
- Department of Clinical Laboratory, Changsha Hospital of Traditional Chinese Medicine (Changsha Eighth Hospital), Changsha, Hunan, People’s Republic of China
| | - Liangyi Xie
- Department of Clinical Laboratory, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People’s Republic of China
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Morton AB, Boyle E, Pettengill MA, Gancher E. The Brief Case: Strictly Anaerobic and Staining Acid Fast. J Clin Microbiol 2023; 61:e0015022. [PMID: 37219093 PMCID: PMC10204630 DOI: 10.1128/jcm.00150-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Affiliation(s)
- Arianna B. Morton
- Thomas Jefferson University Hospital, Department of Pathology, Anatomy, and Cell Biology, Philadelphia, Pennsylvania, USA
| | - Evan Boyle
- Thomas Jefferson University Hospital, Division of Infectious Diseases, Philadelphia, Pennsylvania, USA
| | - Matthew A. Pettengill
- Thomas Jefferson University Hospital, Department of Pathology, Anatomy, and Cell Biology, Philadelphia, Pennsylvania, USA
| | - Elizabeth Gancher
- Thomas Jefferson University Hospital, Division of Infectious Diseases, Philadelphia, Pennsylvania, USA
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Zhou F, Zhang J, Gong L, Wang G, Khan A, Cui H. Infection caused by Lawsonella clevelandensis after breast augmentation with autologous fat grafting: a case report. BMC Infect Dis 2023; 23:124. [PMID: 36855087 PMCID: PMC9976391 DOI: 10.1186/s12879-022-07812-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 10/26/2022] [Indexed: 03/02/2023] Open
Abstract
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.
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Affiliation(s)
- Feng Zhou
- grid.412793.a0000 0004 1799 5032Department of Plastic and Aesthetic Surgery, Tongji Hospital Affiliated to Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065 China
| | - Jun Zhang
- grid.412793.a0000 0004 1799 5032Department of Plastic and Aesthetic Surgery, Tongji Hospital Affiliated to Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065 China
| | - Lunli Gong
- grid.412793.a0000 0004 1799 5032Department of Plastic and Aesthetic Surgery, Tongji Hospital Affiliated to Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065 China
| | - Guobao Wang
- grid.412793.a0000 0004 1799 5032Department of Plastic and Aesthetic Surgery, Tongji Hospital Affiliated to Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065 China
| | - Aawrish Khan
- grid.412793.a0000 0004 1799 5032Department of Plastic and Aesthetic Surgery, Tongji Hospital Affiliated to Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065 China
| | - Haiyan Cui
- Department of Plastic and Aesthetic Surgery, Tongji Hospital Affiliated to Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065, China.
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Lawsonella clevelandensis, a case series of vascular graft infections caused by a rare pathogen. IDCases 2023; 31:e01735. [PMID: 36911869 PMCID: PMC9992747 DOI: 10.1016/j.idcr.2023.e01735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/02/2023] [Accepted: 03/05/2023] [Indexed: 03/08/2023] Open
Abstract
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.
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5
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Ahmed W, Dewar S, Williams R, Stansby G, Harris K, Weiand D. Lawsonella clevelandensis is a rare cause of infected chronic contained rupture of abdominal aortic aneurysm. Access Microbiol 2021; 3:acmi000183. [PMID: 33997614 PMCID: PMC8115980 DOI: 10.1099/acmi.0.000183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 11/09/2020] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Wissam Ahmed
- Freeman Hospital, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK
| | - Simon Dewar
- Freeman Hospital, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK
| | - Robin Williams
- Freeman Hospital, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK
| | - Gerard Stansby
- Freeman Hospital, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK
| | - Kathryn Harris
- Great Ormond Street Hospital, Great Ormond St., Holborn, London WC1N 3JH, UK
| | - Daniel Weiand
- Freeman Hospital, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK
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Ramesh R, Assi M, Esquer Garrigos Z, Sohail MR. Lawsonella clevelandensis: an emerging cause of vascular graft infection. BMJ Case Rep 2021; 14:14/2/e237350. [PMID: 33637490 PMCID: PMC7919573 DOI: 10.1136/bcr-2020-237350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
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.
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Affiliation(s)
- Rommel Ramesh
- Charles University Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic,Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Mariam Assi
- Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Zerelda Esquer Garrigos
- Mayo Clinic Rochester, Rochester, Minnesota, USA,Division of Infectious Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
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7
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Gonzales Zamora JA, Romero Alvarez M, Henry Z, Baracco GJ, Dickinson G, Lichtenberger P. Liver abscess caused by Lawsonella clevelandensis in a patient with rheumatoid arthritis: A case report and literature review. IDCases 2020; 20:e00734. [PMID: 32154106 PMCID: PMC7057191 DOI: 10.1016/j.idcr.2020.e00734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/26/2020] [Accepted: 02/26/2020] [Indexed: 12/14/2022] Open
Abstract
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.
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Affiliation(s)
- Jose A Gonzales Zamora
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, United States
| | - Maria Romero Alvarez
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, United States
| | - Zachary Henry
- The AIDS Healthcare Foundation, Northpoint Health Center, Fort Lauderdale, FL, 33308, United States
| | - Gio J Baracco
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, United States.,Department of Infectious Diseases, Miami Veterans Affairs Healthcare System, Miami, FL, 33125, United States
| | - Gordon Dickinson
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, United States.,Department of Infectious Diseases, Miami Veterans Affairs Healthcare System, Miami, FL, 33125, United States
| | - Paola Lichtenberger
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, United States.,Department of Infectious Diseases, Miami Veterans Affairs Healthcare System, Miami, FL, 33125, United States
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8
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Gudivada V, Gochhait D, Bhandary C, Mishra N, Siddaraju N. Cutaneous nocardiosis with discharging sinus clinically mimicking tuberculosis diagnosed by cytology. Diagn Cytopathol 2019; 47:935-938. [PMID: 31173479 DOI: 10.1002/dc.24217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/19/2019] [Accepted: 05/22/2019] [Indexed: 11/11/2022]
Abstract
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.
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Affiliation(s)
- Vijayalakshmi Gudivada
- Department of Pathology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Debasis Gochhait
- Department of Pathology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Chandni Bhandary
- Department of Pathology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Nimesh Mishra
- Department of Pathology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Neelaiah Siddaraju
- Department of Pathology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
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9
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Gonzalez E, Pitre FE, Brereton NJB. ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples. Environ Microbiol 2019; 21:2440-2468. [PMID: 30990927 PMCID: PMC6851558 DOI: 10.1111/1462-2920.14632] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/07/2019] [Accepted: 04/15/2019] [Indexed: 01/04/2023]
Abstract
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.
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Affiliation(s)
- Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, H3A 0G1, Canada.,Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada
| | - Frederic E Pitre
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.,Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - Nicholas J B Brereton
- Institut de Recherche en Biologie Végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
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10
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Munson E, Carroll KC. An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017. J Clin Microbiol 2019; 57:e01181-18. [PMID: 30257907 PMCID: PMC6355528 DOI: 10.1128/jcm.01181-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
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.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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11
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Kumaria A, Lucas EK, Crusz SA, Howarth SPS, Cartmill M. Lawsonella clevelandensis causing spinal subdural empyema. Br J Neurosurg 2018:1-3. [PMID: 30451005 DOI: 10.1080/02688697.2018.1540767] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
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.
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Affiliation(s)
- A Kumaria
- a Departments of Paediatric Neurosurgery , Queen's Medical Centre , Nottingham , UK
| | - E K Lucas
- a Departments of Paediatric Neurosurgery , Queen's Medical Centre , Nottingham , UK
| | - S A Crusz
- b Microbiology , Queen's Medical Centre , Nottingham , UK
| | - S P S Howarth
- a Departments of Paediatric Neurosurgery , Queen's Medical Centre , Nottingham , UK
| | - M Cartmill
- a Departments of Paediatric Neurosurgery , Queen's Medical Centre , Nottingham , UK
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12
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Escapa IF, Chen T, Huang Y, Gajare P, Dewhirst FE, Lemon KP. New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract. mSystems 2018; 3:e00187-18. [PMID: 30534599 PMCID: PMC6280432 DOI: 10.1128/msystems.00187-18] [Citation(s) in RCA: 301] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/02/2018] [Indexed: 12/22/2022] Open
Abstract
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.
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Affiliation(s)
- Isabel F. Escapa
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Tsute Chen
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Yanmei Huang
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Prasad Gajare
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Floyd E. Dewhirst
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Katherine P. Lemon
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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13
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Favila Menezes M, Sousa MJ, Paixão P, Atouguia J, Negreiros I, Simões MJ. Lawsonella clevelandensis as the causative agent of a breast abscess. IDCases 2018; 12:95-96. [PMID: 29942760 PMCID: PMC6011140 DOI: 10.1016/j.idcr.2018.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 12/01/2022] Open
Abstract
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.
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Affiliation(s)
- M Favila Menezes
- CML Germano de Sousa, Portugal.,Hospital CUF Descobertas, Portugal
| | | | | | | | | | - M J Simões
- Instituto Nacional Dr. Ricardo Jorge, Portugal
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14
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Janda JM. Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2016. Diagn Microbiol Infect Dis 2017; 88:100-105. [PMID: 28238386 DOI: 10.1016/j.diagmicrobio.2017.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/06/2017] [Indexed: 12/22/2022]
Abstract
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.
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Affiliation(s)
- J Michael Janda
- Public Health Laboratory, Public Health Services Department, Kern County, Bakersfield, CA, 93306-3302.
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Navas ME, Jump R, Canaday DH, Wnek MD, SenGupta DJ, McQuiston JR, Bell M. Can anaerobes be acid fast? A novel, clinically relevant acid fast anaerobe. JMM Case Rep 2016; 3:e005036. [PMID: 28348766 PMCID: PMC5330234 DOI: 10.1099/jmmcr.0.005036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/05/2016] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Maria E Navas
- Microbiology Laboratory, Louis Stokes Cleveland Veterans Affairs Medical Center , Cleveland, Ohio , USA
| | - Robin Jump
- Geriatric Research Education and Clinical Center, Louis Stokes Cleveland VAMC, Cleveland, Ohio and Department of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University , Cleveland, Ohio , USA
| | - David H Canaday
- Geriatric Research Education and Clinical Center, Louis Stokes Cleveland VAMC, Cleveland, Ohio and Department of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University , Cleveland, Ohio , USA
| | - Maria D Wnek
- Microbiology Laboratory, Louis Stokes Cleveland Veterans Affairs Medical Center , Cleveland, Ohio , USA
| | - Dhruba J SenGupta
- Department of Laboratory Medicine, University of Washington Medical Center , Seattle, Washington , USA
| | - John R McQuiston
- Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology Centers for Disease Control and Prevention , Atlanta, Georgia , USA
| | - Melissa Bell
- Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology Centers for Disease Control and Prevention , Atlanta, Georgia , USA
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Bell ME, Bernard KA, Harrington SM, Patel NB, Tucker TA, Metcalfe MG, McQuiston JR. Lawsonella clevelandensis gen. nov., sp. nov., a new member of the suborder Corynebacterineae isolated from human abscesses. Int J Syst Evol Microbiol 2016; 66:2929-2935. [PMID: 27130323 DOI: 10.1099/ijsem.0.001122] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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).
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Affiliation(s)
- Melissa E Bell
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kathryn A Bernard
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Department of Medical Microbiology and Infectious Diseases, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Susan M Harrington
- Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nisha B Patel
- Department of Microbiology & Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Trudy-Ann Tucker
- Georgia State University, 24 Peachtree Center Ave, Atlanta, GA 30303, USA
| | - Maureen G Metcalfe
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R McQuiston
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Complete Genome Sequences for Two Strains of a Novel Fastidious, Partially Acid-Fast, Gram-Positive Corynebacterineae Bacterium, Derived from Human Clinical Samples. GENOME ANNOUNCEMENTS 2015; 3:3/6/e01462-15. [PMID: 26659691 PMCID: PMC4675956 DOI: 10.1128/genomea.01462-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
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.
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