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Munson E, Carella A, Carroll KC. Valid and accepted novel bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2022. J Clin Microbiol 2023; 61:e0083823. [PMID: 37889007 PMCID: PMC10662342 DOI: 10.1128/jcm.00838-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
Although some nomenclature changes have caused consternation among clinical microbiologists, the discovery of novel taxa and improving classification of existing groups of organisms is exciting and adds to our understanding of microbial pathogenesis. In this mini-review, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2022. Henceforth, these bacteriology taxonomic summaries will appear annually. Several of the novel Gram-positive organisms have been associated with disease, namely, the Corynebacterium kroppenstedtii-like organisms Corynebacterium parakroppenstedtii sp. nov. and Corynebacterium pseudokroppenstedtii sp. nov. A newly described Streptococcus species, Streptococcus toyakuensis sp. nov., is noteworthy for exhibiting multi-drug resistance. Among the novel Gram-negative pathogens, Vibrio paracholerae sp. nov. stands out as an organism associated with diarrhea and sepsis and has probably been co-circulating with pandemic Vibrio cholerae for decades. Many new anaerobic organisms have been described in this past year largely from genetic assessments of gastrointestinal microbiome collections. With respect to revised taxa, as discussed in previous reviews, the genus Bacillus continues to undergo further division into additional genera and reassignment of existing species into them. Reassignment of two subspecies of Fusobacterium nucleatum to species designations (Fusobacterium animalis sp. nov. and Fusobacterium vincentii sp. nov.) is also noteworthy. As was typical of previous reviews, literature updates for selected clinically relevant organisms discovered between 2017 and 2021 have been included.
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Affiliation(s)
- Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Arianna Carella
- Department of Medical Laboratory Science, 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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2
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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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3
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Ozga AT, Ottoni C. Dental calculus as a proxy for animal microbiomes. QUATERNARY INTERNATIONAL : THE JOURNAL OF THE INTERNATIONAL UNION FOR QUATERNARY RESEARCH 2023; 653-654:47-52. [PMID: 37559969 PMCID: PMC7614904 DOI: 10.1016/j.quaint.2021.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
The field of dental calculus research has exploded in recent years, predominantly due to the multitude of studies related to human genomes and oral pathogens. Despite having a subset of these studies devoted to non-human primates, little progress has been made in the distribution of oral pathogens across domestic and wild animal populations. This overlooked avenue of research is particularly important at present when many animal populations with the potentiality for zoonotic transmission continue to reside in close proximity to human groups due to reasons such as deforestation and climatic impacts on resource availability. Here, we analyze all previously available published oral microbiome data recovered from the skeletal remains of animals, all of which belong to the Mammalia class. Our genus level results emphasize the tremendous diversity of oral ecologies across mammals in spite of the clustering based primarily on host species. We also discuss the caveats and flaws in analyzing ancient animal oral microbiomes at the species level of classification. Lastly, we assess the benefits, challenges, and gaps in the current knowledge of dental calculus research within animals and postulate the future of the field as a whole.
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Affiliation(s)
- Andrew T. Ozga
- Nova Southeastern University, Halmos College of Arts and Sciences, Fort Lauderdale, FL, 33314, USA
| | - Claudio Ottoni
- DANTE - Diet and ANcient TEchnology Laboratory, Department of Oral and Maxillo-Facial Sciences, “Sapienza” University of Rome, 00161, Rome, Italy
- Centre of Molecular Anthropology for Ancient DNA Studies; Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
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4
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Maev IV, Levchenko AI, Galeeva JS, Andreev DN, Osipenko JV, Bordin DS, Ilyina EN. [Comparative analysis of the intestinal microbiota in patients with exocrine pancreatic insufficiency of various severity]. TERAPEVT ARKH 2023; 95:130-139. [PMID: 37167128 DOI: 10.26442/00403660.2023.02.202056] [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: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Exocrine pancreatic insufficiency (EPI) is a critical host factor in determining the composition of the gut microbiota. Diseases that cause exocrine insufficiency can affect the gut microbiome, which can potentiate disease progression and complications. To date, the relationship of exocrine insufficiency in various pancreatic (PA) pathologies, in chronic pancreatitis (CP), with dysbiotic changes in the intestinal microbiota (IM) has not been reliably studied. The available data are heterogeneous and contradictory, which determines the need for further research. AIM To conduct a comparative analysis of the taxonomic composition of the intestinal microbiota in patients with CP of various etiologies, without or with the presence of EPI of varying severity, as well as patients with severe EPI with a history of surgical intervention (SI) on the pancreas. MATERIALS AND METHODS A total of 85 patients were included in the study. Patients were divided into groups according to the severity of EPI: Group 1 (n=16) - patients with CP without EPI; Group 2 (n=11) - patients with CP and mild EPI; Group 3 (n=17) - patients with severe CP and EPI; Group 4 (n=41) - severe EPI in persons with a history of SI on the pancreas. Verification of CP was carried out according to clinical, anamnestic and instrumental data. The degree of EPI was determined by the level of pancreatic elastase-1 (PE-1) feces. Informed consent for the study was obtained for each patient, an anamnesis was collected, physical and laboratory examinations were performed, and a stool sample was obtained. DNA was extracted from each stool sample, the taxonomic composition of BM was determined by sequencing the bacterial 16S rRNA genes, followed by bioinformatic analysis. RESULTS We followed the changes in the gut microbiota from a group of patients with CP without EPI to a group with severe EPI, in those who underwent SI. At the level of the phylum, the IM of all groups showed the dominance of Firmicutes, with the lowest representation in the severe EPI group, both with SI and CP, and the growth of the Actinobacteria, Verrucomicrobiota and Fusobacteria types. The differential representation of childbirth varied: in patients with severe EPI and CP, compared with mild, statistically significant genera - Akkermansia, Ruminococcus gauvreauii group and Holdemanella; compared with CP without exocrine insufficiency, Prevotella, Ruminococcus gauvreauii group, Peptostreptococcus and Blautia dominated. The CP group with mild EPI was dominated by the following genera: Lachnospiraceae_ND 2004 group, Faecalitalea, Fusobacterium, Catenibacterium, Roseburia, Atopobium, Cloacibacillus, Clostridium innococum group, Ruminococcus torques group. All groups showed a low diversity of taxa with a predominance of opportunistic flora, including participants in oncogenesis. CONCLUSION The results of the study show that patients with CP of various etiologies and patients with severe EPI who underwent specific intervention on the pancreas have intestinal microbiota dysbiosis, the severity of which is significantly influenced by the degree of EPI.
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Affiliation(s)
- I V Maev
- Yevdokimov Moscow State University of Medicine and Dentistry
| | - A I Levchenko
- Yevdokimov Moscow State University of Medicine and Dentistry
| | - J S Galeeva
- Research Institute for Systems Biology and Medicine
| | - D N Andreev
- Yevdokimov Moscow State University of Medicine and Dentistry
| | | | - D S Bordin
- Yevdokimov Moscow State University of Medicine and Dentistry
- Loginov Moscow Clinical Scientific Center
- Tver State Medical University
| | - E N Ilyina
- Research Institute for Systems Biology and Medicine
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5
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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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7
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Identification of Bull Semen Microbiome by 16S Sequencing and Possible Relationships with Fertility. Microorganisms 2021; 9:microorganisms9122431. [PMID: 34946031 PMCID: PMC8705814 DOI: 10.3390/microorganisms9122431] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 01/04/2023] Open
Abstract
Reports on the use of 16S sequencing for the identification of bacteria in healthy animals are lacking. Bacterial contamination of bull semen can have a negative effect on the sperm quality. The aims of this study were threefold: to identify bacteria in the semen of healthy bulls using 16S sequencing; to investigate the differences in the bacterial community between individual bulls; and to establish if there was a relationship between the bacteria isolated and bull fertility. Semen from 18 bulls of known fertility was used for the DNA extraction and 16S sequencing; 107 bacterial genera were identified. The differences in the amplicon sequence variants (ASVs) and the numbers of genera between bulls were noted. Negative correlations (p < 0.05) between several bacterial genera with Curvibacter, Rikenellaceae RC9-gut-group and Dyella spp. were seen. Other negatively correlated bacteria were Cutibacterium, Ruminococcaceae UCG-005, Ruminococcaceae UCG-010 and Staphylococcus, all within the top 20 genera. Two genera, W5053 and Lawsonella, were enriched in bulls of low fertility; this is the first time that these bacteria have been reported in bull semen samples. The majority of the bacteria were environmental organisms or were species originating from the mucous membranes of animals and humans. The results of this study indicate that differences in the seminal microbiota of healthy bulls occur and might be correlated with fertility.
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8
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C Campbell B, Gong S, Greenfield P, J Midgley D, T Paulsen I, C George S. Aromatic compound-degrading taxa in an anoxic coal seam microbiome from the Surat Basin, Australia. FEMS Microbiol Ecol 2021; 97:6206826. [PMID: 33791788 DOI: 10.1093/femsec/fiab053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Methane is an important energy resource internationally, and a large proportion of this methane is produced by microbial communities living in coal seams. Despite the value of this resource for human energy security, our understanding of the metabolic roles played by specific taxa during the biodegradation of coal to methane in situ is quite limited. In order to develop a greater understanding of microbial catabolism on coal, a community from a coal seam in the Surat Basin, Australia, was incubated on 10 different aromatic organic compounds: coronene, benzo[a]pyrene, pyrene, phenanthrene, naphthalene, ethylbenzene, phenol, benzoate, vanillate and syringate. Each of these aromatic compounds either occurs in coal or is a possible product of the coal biodegradation process. 16S rRNA sequencing revealed substantial changes to each community in response to each aromatic carbon substrate provided. Abundant taxa from these substrate-specific communities were identified and their probable catabolic roles proposed based on literature searches of related taxa. This study is the first to link specific coal seam taxa to aromatic substrates available in coal seam environments. Two conceptual models of the putative degradation pathways and key taxa responsible are proposed.
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Affiliation(s)
- Bronwyn C Campbell
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia.,Department of Earth and Environmental Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Se Gong
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Paul Greenfield
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - David J Midgley
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Simon C George
- Department of Earth and Environmental Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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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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10
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Gamba RR, Koyanagi T, Peláez AL, De Antoni G, Enomoto T. Changes in Microbiota During Multiple Fermentation of Kefir in Different Sugar Solutions Revealed by High-Throughput Sequencing. Curr Microbiol 2021; 78:2406-2413. [PMID: 33961093 DOI: 10.1007/s00284-021-02501-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
Kefir is a fermented beverage produced through the activity of its grains, which is constituted by lactic acid and acetic acid bacteria and yeasts. We studied the bacterial succession during multiple fermentation of Argentinian kefir in brown sugar, purified molasses or high-test molasses, using 16S high-throughput sequencing. Firmicutes was dominant (up to 98% of total population) in grains and beverages made from various sugar substrates, except in high-test molasses beverage, which was dominated by Proteobacteria (up to 78% of total population). Major bacterial species in Firmicutes were Liquorilactobacillus nagelii, Lentilactobacillus hilgardii/diolivorans and Lacticaseibacillus casei/paracasei, which are active in lactic acid fermentation. Proteobacteria comprised Acetobacter lovaniensis and Gluconobacter oxydans/roseus as major species, which are presumably responsible for the acetic acid formation in sugary kefir beverages. Bacteria differ in abundance depending on the sugar type, as revealed by the competitive dominances between L. nagelii and A. loveniensis. Purified molasses led to scarce acetic acid bacteria during fermentation, indicating that it is not a suitable substrate for their growth. Our results suggest that acetic acid (and/or ethanol) in sugary kefir modulates the succession and dominance of specific lactic acid bacteria. This study will provide valuable information for designing more sophisticated non-dairy fermented beverages with stable microbial properties.
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Affiliation(s)
- Raúl Ricardo Gamba
- Department of Food Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
| | - Takashi Koyanagi
- Department of Food Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
| | - Angela León Peláez
- Facultad de Ciencias Exactas, Cátedra de Microbiología, Universidad Nacional de La Plata, Calle 47 y 115, 1900, La Plata, Argentina
| | - Graciela De Antoni
- Facultad de Ciencias Exactas, Cátedra de Microbiología, Universidad Nacional de La Plata, Calle 47 y 115, 1900, La Plata, Argentina
| | - Toshiki Enomoto
- Department of Food Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan.
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11
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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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12
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Watanabe K, Yamada A, Nishi Y, Tashiro Y, Sakai K. Relationship between the bacterial community structures on human hair and scalp. Biosci Biotechnol Biochem 2020; 84:2585-2596. [PMID: 32993459 DOI: 10.1080/09168451.2020.1809989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, we investigated and compared characteristics of the bacterial community structures on hair (scalp hair) and scalp in 18 individuals. Significant differences were found between the sites, in terms of cell density, alpha and beta diversity, and relative abundance of the phyla, Firmicutes and Proteobacteria, whereas no difference was found in relative abundance of the phylum Actinobacteria. Bacteria of the genus Cutibacterium showed similar relative abundance at both sites, whereas those of genus Pseudomonas were highly abundant on hair, and those of genus Staphylococcus were significantly lesser in abundance on hair than on scalp. Statistical correlations between the sites were high for the individual relative abundance of five major operational taxonomic units (OTUs). This suggests that the bacterial community structure on hair is composed of hair-specific genus, Pseudomonas, and skin-derived genera, Cutibacterium and Staphylococcus, and is distinguishable from other human skin microbiomes.
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Affiliation(s)
- Kota Watanabe
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University , Fukuoka, Japan
| | - Azusa Yamada
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University , Fukuoka, Japan
| | - Yuri Nishi
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University , Fukuoka, Japan
| | - Yukihiro Tashiro
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University , Fukuoka, Japan.,Laboratory of Microbial Environmental Protection, Tropical Microbiology Unit, Center for International Education and Research of Agriculture, Faculty of Agriculture, Kyushu University , Fukuoka, Japan
| | - Kenji Sakai
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University , Fukuoka, Japan.,Laboratory of Microbial Environmental Protection, Tropical Microbiology Unit, Center for International Education and Research of Agriculture, Faculty of Agriculture, Kyushu University , Fukuoka, Japan
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13
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Liwinski T, Zenouzi R, John C, Ehlken H, Rühlemann MC, Bang C, Groth S, Lieb W, Kantowski M, Andersen N, Schachschal G, Karlsen TH, Hov JR, Rösch T, Lohse AW, Heeren J, Franke A, Schramm C. Alterations of the bile microbiome in primary sclerosing cholangitis. Gut 2020; 69:665-672. [PMID: 31243055 DOI: 10.1136/gutjnl-2019-318416] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/03/2019] [Accepted: 06/06/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Patients with primary sclerosing cholangitis (PSC) display an altered colonic microbiome compared with healthy controls. However, little is known on the bile duct microbiome and its interplay with bile acid metabolism in PSC. METHODS Patients with PSC (n=43) and controls without sclerosing cholangitis (n=22) requiring endoscopic retrograde cholangiography were included prospectively. Leading indications in controls were sporadic choledocholithiasis and papillary adenoma. A total of 260 biospecimens were collected from the oral cavity, duodenal fluid and mucosa and ductal bile. Microbiomes of the upper alimentary tract and ductal bile were profiled by sequencing the 16S-rRNA-encoding gene (V1-V2). Bile fluid bile acid composition was measured by high-performance liquid chromatography mass spectrometry and validated in an external cohort (n=20). RESULTS The bile fluid harboured a diverse microbiome that was distinct from the oral cavity, the duodenal fluid and duodenal mucosa communities. The upper alimentary tract microbiome differed between PSC patients and controls. However, the strongest differences between PSC patients and controls were observed in the ductal bile fluid, including reduced biodiversity (Shannon entropy, p=0.0127) and increase of pathogen Enterococcus faecalis (FDR=4.18×10-5) in PSC. Enterococcus abundance in ductal bile was strongly correlated with concentration of the noxious secondary bile acid taurolithocholic acid (r=0.60, p=0.0021). CONCLUSION PSC is characterised by an altered microbiome of the upper alimentary tract and bile ducts. Biliary dysbiosis is linked with increased concentrations of the proinflammatory and potentially cancerogenic agent taurolithocholic acid.
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Affiliation(s)
- Timur Liwinski
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Roman Zenouzi
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Clara John
- Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hanno Ehlken
- Department of Interdisciplinary Endoscopy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malte C Rühlemann
- Christian-Albrechts-Universität zu Kiel, Institute of Clinical Molecular Biology, Kiel, Germany
| | - Corinna Bang
- Institute for Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Stefan Groth
- Department of Interdisciplinary Endoscopy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Marcus Kantowski
- Department of Interdisciplinary Endoscopy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nils Andersen
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Schachschal
- Department of Interdisciplinary Endoscopy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tom H Karlsen
- Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Johannes R Hov
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Thomas Rösch
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ansgar W Lohse
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joerg Heeren
- Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andre Franke
- Institute for Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Christoph Schramm
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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14
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Fritz B, März M, Weis S, Wahl S, Ziemssen F, Egert M. Site-specific molecular analysis of the bacteriota on worn spectacles. Sci Rep 2020; 10:5577. [PMID: 32221361 PMCID: PMC7101307 DOI: 10.1038/s41598-020-62186-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 03/05/2020] [Indexed: 02/06/2023] Open
Abstract
Regularly touched surfaces are usually contaminated with microorganisms and might be considered as fomites. The same applies for spectacles, but only little is known about their microbial colonization. Previous cultivation-based analyses from our group revealed a bacterial load strongly dominated by staphylococci. To better account for aerotolerant anaerobes, slow growing and yet-uncultivated bacteria, we performed an optimized 16S rRNA gene sequencing approach targeting the V1-V3 region. 30 spectacles were swab-sampled at three sites, each (nosepads, glasses and earclips). We detected 5232 OTUs affiliated with 19 bacterial phyla and 665 genera. Actinobacteria (64%), Proteobacteria (22%), Firmicutes (7%) and Bacteroidetes (5%) were relatively most abundant. At genus level, 13 genera accounted for 84% of the total sequences of all spectacles, having a prevalence of more than 1% relative abundance. Propionibacterium (57%), Corynebacterium (5%), Staphylococcus (4%), Pseudomonas, Sphingomonas and Lawsonella (3%, each) were the dominant genera. Interestingly, bacterial diversity on the glasses was significantly higher compared to nosepads and earclips. Our study represents the first cultivation-independent study of the bacteriota of worn spectacles. Dominated by bacteria of mostly human skin and epithelia origin and clearly including potential pathogens, spectacles may play a role as fomites, especially in clinical environments.
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Affiliation(s)
- Birgit Fritz
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054, Villingen-Schwenningen, Germany
| | - Melanie März
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054, Villingen-Schwenningen, Germany
| | - Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054, Villingen-Schwenningen, Germany
| | - Siegfried Wahl
- Institute for Ophthalmic Research, Eberhard-Karls University, Elfriede-Aulhorn-Straße 7, 72076, Tuebingen, Germany
| | - Focke Ziemssen
- Center for Ophthalmology, Eberhard-Karls University, Elfriede-Aulhorn-Straße 7, 72076, Tuebingen, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054, Villingen-Schwenningen, Germany.
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15
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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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16
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Goldenberger D, Naegele M, Steffens D, Eichenberger R, Egli A, Seth-Smith H. Emerging anaerobic and partially acid-fast Lawsonella clevelandensis: extended characterization by antimicrobial susceptibility testing and whole genome sequencing. Clin Microbiol Infect 2019; 25:1447-1448. [DOI: 10.1016/j.cmi.2019.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 06/25/2019] [Accepted: 07/04/2019] [Indexed: 11/17/2022]
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17
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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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18
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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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19
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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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20
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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: 294] [Impact Index Per Article: 49.0] [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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21
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Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 394] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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22
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Baek I, Kim M, Lee I, Na SI, Goodfellow M, Chun J. Phylogeny Trumps Chemotaxonomy: A Case Study Involving Turicella otitidis. Front Microbiol 2018; 9:834. [PMID: 29760685 PMCID: PMC5936774 DOI: 10.3389/fmicb.2018.00834] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/12/2018] [Indexed: 11/13/2022] Open
Abstract
The genus Turicella was proposed to harbor clinical strains isolated from middle-ear fluids of patients with otitis media. 16S rRNA phylogeny showed that it belonged to the mycolic acid-containing actinobacteria, currently classified in the order Corynebacteriales, and was closely related to the genus Corynebacterium. A new genus was proposed for the organisms as unlike corynebacteria they lacked mycolic acids and had different menaquinones. Here, we carried out large-scale comparative genomics on representative strains of the genera Corynebacterium and Turicella to check if this chemotaxonomic classification is justified. Three genes that are known to play an essential role in mycolic acid biosynthesis were absent in Turicella and two other mycolate-less Corynebacterium spp., explaining the lack of mycolic acids resulted from the deletion of genes and does not confer any phylogenetic context. Polyphasic phylogenetic analyses using 16S rRNA, bacterial core genes and genes responsible for synthesizing menaquinones unequivocally indicate that Turicella is a true member of the genus Corynebacterium. Here, we demonstrate that menaquinone and mycolic acid that have been used as critical taxonomic markers should be interpreted carefully, particularly when genome-based taxonomy is readily available. Based on the phylogenetic analysis, we propose to reclassify Turicella otitidis as Corynebacterium otitidis comb. nov.
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Affiliation(s)
- Inwoo Baek
- School of Biological Sciences, Seoul National University, Seoul, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Mincheol Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Imchang Lee
- School of Biological Sciences, Seoul National University, Seoul, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Seong-In Na
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jongsik Chun
- School of Biological Sciences, Seoul National University, Seoul, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
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23
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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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24
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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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