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Karroum PJ, Padda I, Taik S, Piccione G, Fabian D, Kavarthapu A, Tantry B, Mahmoud M, Vandenborn S, Otiwaah J, Diaz K. Atopobium minutum: An uncommon culprit of severe bacteremia and empyema: A case report and literature review. Radiol Case Rep 2024; 19:3915-3921. [PMID: 39040826 PMCID: PMC11261269 DOI: 10.1016/j.radcr.2024.06.020] [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: 05/29/2024] [Accepted: 06/05/2024] [Indexed: 07/24/2024] Open
Abstract
Atopobium minutum (A. minutum) has rarely been documented in human infections. However, this report describes a case involving a 52-year-old woman who developed empyema and lung collapse due to A. minutum. She initially presented to the emergency department with nausea, vomiting, diarrhea, and abdominal pain. Her condition quickly declined within the first day of arrival, leading to respiratory failure and requiring intubation and ICU-level care. Despite receiving intensive antibiotic treatment, the patient needed prolonged intubation and a tracheostomy. Initial cultures indicated Streptococcus intermedius and Lactobacillus minutus, but final culture results identified A. minutum as the cause. This case highlights the difficulty in diagnosing A. minutum infections, often necessitating advanced DNA sequencing, and raises concerns about potential multidrug resistance. It highlights the importance of prompt identification of the pathogen by laboratories to allow for effective treatment of these rare infections.
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Affiliation(s)
- Paul J. Karroum
- Department of Internal Medicine, Richmond University Medical Center/Mount Sinai, Staten Island, NY, USA
| | - Inderbir Padda
- Department of Internal Medicine, Richmond University Medical Center/Mount Sinai, Staten Island, NY, USA
| | - Sophia Taik
- Department of Internal Medicine, Richmond University Medical Center/Mount Sinai, Staten Island, NY, USA
| | - Gianpaolo Piccione
- Department of Internal Medicine, Richmond University Medical Center/Mount Sinai, Staten Island, NY, USA
| | - Daniel Fabian
- Department of Internal Medicine, Richmond University Medical Center/Mount Sinai, Staten Island, NY, USA
| | - Anusha Kavarthapu
- Department of Internal Medicine, Richmond University Medical Center/Mount Sinai, Staten Island, NY, USA
| | - Bhuvana Tantry
- Department of Internal Medicine, Richmond University Medical Center/Mount Sinai, Staten Island, NY, USA
| | - Mahmoud Mahmoud
- Department of Radiology, Richmond University Medical Center/Mount Sinai, Staten Island, NY, USA
| | | | - Juliana Otiwaah
- School of Medicine, St. George's University, True Blue, Grenada
| | - Keith Diaz
- Department of Pulmonary and Critical Care, Richmond University Medical Center/Mount Sinai, Staten Island, NY, USA
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Guta M, Abebe G, Bacha K, Cools P. Screening and characterization of thermostable enzyme-producing bacteria from selected hot springs of Ethiopia. Microbiol Spectr 2024; 12:e0371023. [PMID: 38294247 PMCID: PMC10913744 DOI: 10.1128/spectrum.03710-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024] Open
Abstract
Hot springs are potential sources of diverse arrays of microbes and their thermostable hydrolytic enzymes. Water and sediment samples were collected from three hot springs of Ethiopia and enriched on nutrient and thermus agar media to isolate pure cultures of potential microbes. A total of 252 bacterial isolates were screened and evaluated for the production of amylase, protease, cellulase, and lipase. About 95.23%, 84.12%, 76.58%, and 65.07% of the isolates displayed promising amylase, proteases, cellulase, and lipase activities, respectively. Based on the diameter of the clear zone formed, 45 isolates were further screened and identified to species level using matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry analysis and 16S rRNA gene sequencing. Five of the 45 isolates showed significantly high (P < 0.05) clear zone ratios as compared to others. The identified isolates were categorized under five bacterial species, namely, Bacillus licheniformis, Bacillus cereus, Paenibacillus thiaminolyticus, Paenibacillus dendritiformis, and Brevibacillus borstelensis. The most dominant species (66.7%) was B. licheniformis. It could be concluded that hot springs of Ethiopia are potential sources of thermostable extracellular hydrolytic enzymes for various industrial applications. Further optimization of the growth conditions and evaluation for better productivity of the desired products is recommended before attempting for large-scale production of the hydrolytic enzymes. IMPORTANCE Thermostable microbial enzymes play an important role in industries due to their stability under harsh environmental conditions, including extreme temperatures. Despite their huge application in different industries, however, the thermostable enzymes of thermophilic microorganism origin have not yet been fully explored in Ethiopia. Here, we explored thermophilic bacteria and their enzymes from selected hot spring water and sediment samples. Accordingly, thermophilic bacteria were isolated and screened for the production of extracellular hydrolytic enzymes. Promising numbers of isolates were found as producers of the enzymes. The potent enzyme producers were further identified using matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry analysis and 16S rRNA gene sequencing. The findings revealed the presence of potential hydrolytic enzyme-producing thermophilic bacteria in hot springs of Ethiopia and necessitate further comprehensive study involving other extreme environments. Our findings also revealed the potential of Ethiopian hot springs in the production of thermostable enzymes of significant application in different industries, including food industries.
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Affiliation(s)
- Meseret Guta
- Department of Biology, Jimma University, Jimma, Ethiopia
| | - Genet Abebe
- Department of Biology, Jimma University, Jimma, Ethiopia
| | - Ketema Bacha
- Department of Biology, Jimma University, Jimma, Ethiopia
| | - Piet Cools
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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3
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Morinaga K, Kusada H, Sakamoto S, Murakami T, Toyoda A, Mori H, Meng XY, Takashino M, Murotomi K, Tamaki H. Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two strictly anaerobic, Gram-stain-positive, non-motile bacteria (strains OPF53T and TOC12T) were isolated from mouse intestines. Strains OPF53T and TOC12T grew at pH 5.5–9.0 and 5.0–9.0, respectively, and at temperatures of 30–45 °C. The cell morphologies of these strains were short rods and rods, respectively, and the cells possessed intracellular granules. The major cellular fatty acids of OPF53T were C18 : 1
cis 9 and C18 : 1
cis 9 dimethyl acetal, whereas those of TOC12T were C18 : 0 and C18 : 1
cis 9. In OPF53T, the main end-products of modified peptone–yeast extract–glucose (PYG) fermentation were lactate, formate and butyrate, whereas, in addition to these acids, TOC12T also produced hydrogen. The genomes of OPF53T and TOC12T were respectively 2.2 and 2.0 Mbp in size with a DNA G+C contents of 69.1 and 58.7 %. The 16S rRNA gene sequences of OPF53T and TOC12T showed the highest similarity to members of the family
Atopobiaceae
, namely,
Olsenella phocaeensis
Marseille-P2936T (94.3 %) and
Olsenella umbonata
KCTC 15140T (93.2 %), respectively. Phylogenetic analyses revealed that both isolates formed distinct lineages from other genera of the family
Atopobiaceae
. In addition, the two strains were characterized by relatively low 16S rRNA gene sequence similarity (93.4 %) and can be distinguished by their distinctive traits (including cell shape, DNA G+C content, and major fatty acids profiles). On the basis of their polyphasic taxonomic properties, these isolates represent two noel species of two novel genera within the family
Atopobiaceae
, for which the names Granulimonas faecalis gen. nov., sp. nov. (OPF53T=JCM 35015T=KCTC 25474T) and Leptogranulimonas caecicola gen. nov., sp. nov. (TOC12T=JCM 35017T=KCTC 25472T) are proposed.
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Affiliation(s)
- Kana Morinaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hiroyuki Kusada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Sachiko Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Takumi Murakami
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Hiroshi Mori
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Motoko Takashino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Kazutoshi Murotomi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
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Hooper MJ, LeWitt TM, Veon FL, Pang Y, Chlipala GE, Feferman L, Green SJ, Sweeney D, Bagnowski KT, Burns MB, Seed PC, Guitart J, Zhou XA. Nasal Dysbiosis in Cutaneous T-Cell Lymphoma Is Characterized by Shifts in Relative Abundances of Non- Staphylococcus Bacteria. JID INNOVATIONS 2022; 2:100132. [PMID: 36161104 PMCID: PMC9500465 DOI: 10.1016/j.xjidi.2022.100132] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 12/26/2022] Open
Abstract
The nasal microbiome of patients with cutaneous T-cell lymphoma (CTCL) remains unexplored despite growing evidence connecting nasal bacteria to skin health and disease. Nasal swabs from 45 patients with CTCL (40 with mycosis fungoides, 5 with Sézary syndrome) and 20 healthy controls from the same geographical region (Chicago Metropolitan Area, Chicago, IL) were analyzed using sequencing of 16S ribosomal RNA and tuf2 gene amplicons. Nasal α-diversity did not differ between mycosis fungoides/Sézary syndrome and healthy controls (Shannon index, genus level, P = 0.201), but distinct microbial communities were identified at the class (R2 = 0.104, P = 0.023) and order (R2 = 0.0904, P = 0.038) levels. Increased relative abundance of the genera Catenococcus, Vibrio, Roseomonas, Acinetobacter, and unclassified Clostridiales was associated with increased skin disease burden (P < 0.005, q < 0.05). Performed to accurately resolve nasal Staphylococcus at the species level, tuf2 gene amplicon sequencing revealed no significant differences between mycosis fungoides/Sézary syndrome and healthy controls. Although S. aureus has been shown to worsen CTCL through its toxins, no increase in the relative abundance of this taxon was observed in nasal samples. Despite the lack of differences in Staphylococcus, the CTCL nasal microbiome was characterized by shifts in numerous other bacterial taxa. These data add to our understanding of the greater CTCL microbiome and provide context for comprehending nasal-skin and host‒tumor‒microbial relationships.
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Affiliation(s)
- Madeline J. Hooper
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tessa M. LeWitt
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Francesca L. Veon
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Yanzhen Pang
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - George E. Chlipala
- Research Informatics Core, Research Resources Center, University of Illinois Chicago, Chicago, Illinois, USA
| | - Leo Feferman
- Research Informatics Core, Research Resources Center, University of Illinois Chicago, Chicago, Illinois, USA
| | - Stefan J. Green
- Rush Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, Illinois, USA
| | - Dagmar Sweeney
- Genome Research Core, Genome Research Division, Research Resources Center, University of Illinois Chicago, Chicago, Illinois, USA
| | - Katherine T. Bagnowski
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Michael B. Burns
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Patrick C. Seed
- Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Joan Guitart
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Xiaolong A. Zhou
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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First report of a prosthetic joint infection with Fannyhessea (Atopobium) vaginae. Eur J Clin Microbiol Infect Dis 2022; 41:1023-1027. [PMID: 35610391 DOI: 10.1007/s10096-022-04461-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/16/2022] [Indexed: 11/03/2022]
Abstract
This case describes a 77-year-old woman with dysregulated type II diabetes, presenting with a prosthetic joint infection and bacteremia. Computed tomography (CT) of the pelvis and sacrum revealed manifest periprosthetic collections, suggestive of a septic arthritis with loosening of the hip prosthesis. Synovial fluid grew Fannyhessea vaginae, identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). To our knowledge, this is the first report of a prosthetic joint infection due to this organism.
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Arcos SC, Lira F, Robertson L, González MR, Carballeda-Sangiao N, Sánchez-Alonso I, Zamorano L, Careche M, Jiménez-Ruíz Y, Ramos R, Llorens C, González-Muñoz M, Oliver A, Martínez JL, Navas A. Metagenomics Analysis Reveals an Extraordinary Inner Bacterial Diversity in Anisakids (Nematoda: Anisakidae) L3 Larvae. Microorganisms 2021; 9:1088. [PMID: 34069371 PMCID: PMC8158776 DOI: 10.3390/microorganisms9051088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022] Open
Abstract
L3 larvae of anisakid nematodes are an important problem for the fisheries industry and pose a potential risk for human health by acting as infectious agents causing allergies and as potential vectors of pathogens and microrganisms. In spite of the close bacteria-nematode relationship very little is known of the anisakids microbiota. Fresh fish could be contaminated by bacteria vectored in the cuticle or in the intestine of anisakids when the L3 larvae migrate through the muscles. As a consequence, the bacterial inoculum will be spread, with potential effects on the quality of the fish, and possible clinical effects cannot be discarded. A total of 2,689,113 16S rRNA gene sequences from a total of 113 L3 individuals obtained from fish captured along the FAO 27 fishing area were studied. Bacteria were taxonomically characterized through 1803 representative operational taxonomic units (OTUs) sequences. Fourteen phyla, 31 classes, 52 orders, 129 families and 187 genera were unambiguously identified. We have found as part of microbiome an average of 123 OTUs per L3 individual. Diversity indices (Shannon and Simpson) indicate an extraordinary diversity of bacteria at an OTU level. There are clusters of anisakids individuals (samples) defined by the associated bacteria which, however, are not significantly related to fish hosts or anisakid taxa. This suggests that association or relationship among bacteria in anisakids, exists without the influence of fishes or nematodes. The lack of relationships with hosts of anisakids taxa has to be expressed by the association among bacterial OTUs or other taxonomical levels which range from OTUs to the phylum level. There are significant biological structural associations of microbiota in anisakid nematodes which manifest in clusters of bacteria ranging from phylum to genus level, which could also be an indicator of fish contamination or the geographic zone of fish capture. Actinobacteria, Aquificae, Firmicutes, and Proteobacteria are the phyla whose abundance value discriminate for defining such structures.
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Affiliation(s)
- Susana C. Arcos
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
| | - Felipe Lira
- Centro Nacional de Biotecnología, Departamento de Biotecnología Microbiana, CSIC, 28049 Madrid, Spain; (F.L.); (J.L.M.)
| | - Lee Robertson
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
- Departamento de Protección Vegetal, INIA, 28040 Madrid, Spain
| | - María Rosa González
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
| | | | - Isabel Sánchez-Alonso
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición, CSIC, 28040 Madrid, Spain; (I.S.-A.); (M.C.)
| | - Laura Zamorano
- Servicio de Microbiología y Unidad de Investigación, Hospital Son Espases, (IdISPa), 07120 Palma de Mallorca, Spain; (L.Z.); (A.O.)
| | - Mercedes Careche
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición, CSIC, 28040 Madrid, Spain; (I.S.-A.); (M.C.)
| | - Yolanda Jiménez-Ruíz
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
| | - Ricardo Ramos
- Unidad de Genómica, “Scientific Park of Madrid”, Campus de Cantoblanco, 28049 Madrid, Spain;
| | - Carlos Llorens
- Biotechvana, “Scientific Park”, University of Valencia, 46980 Valencia, Spain;
| | - Miguel González-Muñoz
- Servicio de Immunología, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.C.-S.); (M.G.-M.)
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Son Espases, (IdISPa), 07120 Palma de Mallorca, Spain; (L.Z.); (A.O.)
| | - José L. Martínez
- Centro Nacional de Biotecnología, Departamento de Biotecnología Microbiana, CSIC, 28049 Madrid, Spain; (F.L.); (J.L.M.)
| | - Alfonso Navas
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
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Bordigoni A, Lo C, Yimagou EK, Nicaise B, Diop K, Raoult D, Desnues C, Fenollar F. Two new bacteria isolated from vagina of a patient with vaginosis: Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov. New Microbes New Infect 2020; 38:100771. [PMID: 33204431 PMCID: PMC7652708 DOI: 10.1016/j.nmni.2020.100771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/09/2020] [Accepted: 09/27/2020] [Indexed: 12/21/2022] Open
Abstract
Two new bacterial strains, Marseille-P4126 (=CSURP4126) and Marseille-P4593 (=CSURP4593), were isolated from the vaginal sample of a French woman with vaginosis. These strains were identified and characterized using the taxonogenomics method. The findings from phylogenetic tree interpretation, phenotypic criteria and genomic analysis provided here distinctly display that Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov. are new members of the genus Atopobium and Butyricimonas, respectively.
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Affiliation(s)
- A. Bordigoni
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - E. Kuete Yimagou
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - B. Nicaise
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - K. Diop
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C. Desnues
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
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8
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Mansell J, Gourtsoyannis Y, Draz N, Buchanan R. Infective endocarditis due to Atopobium vaginae: a rare association between genital infection and endocarditis of the tricuspid valve. BMJ Case Rep 2018; 2018:bcr-2018-225871. [PMID: 30173134 PMCID: PMC6120612 DOI: 10.1136/bcr-2018-225871] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2018] [Indexed: 11/04/2022] Open
Abstract
Atopobium vaginae is an anaerobic gram-positive organism associated with genitourinary infections. Bacteraemia is rare, with only two cases reported in the literature. This case describes an 18-year-old type 1 diabetic, presenting with sepsis and haemoptysis, on a background of poor dental hygiene and recurrent hospital admissions. Blood cultures grew A. vaginae and echocardiogram revealed a large tricuspid valve lesion. Despite medical therapy, symptoms of pulmonary emboli continued and she therefore underwent surgical resection of the lesion. Histopathological findings were of a vegetation; culture of the lesion was negative but 16S ribosomal PCR was positive, detecting 16S rRNA of A. vaginae The patient was treated with 4 weeks of vancomycin and made a good recovery. To our knowledge, this represents the first report of infective endocarditis due to this organism. We also provide a review of the literature, including comparing published drug susceptibility data with consensus breakpoints for antimicrobial agents.
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Affiliation(s)
| | - Yannis Gourtsoyannis
- Department of Microbiology, North Middlesex University Hospital NHS Trust, London, UK
| | - Nehal Draz
- Department of Virology, Royal Free Hospital, London, UK
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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: 421] [Impact Index Per Article: 70.2] [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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Diop K, Diop A, Bretelle F, Cadoret F, Michelle C, Richez M, Cocallemen JF, Raoult D, Fournier PE, Fenollar F. Olegusella massiliensis gen. nov., sp. nov., strain KHD7 T, a new bacterial genus isolated from the female genital tract of a patient with bacterial vaginosis. Anaerobe 2017; 44:87-95. [PMID: 28223255 DOI: 10.1016/j.anaerobe.2017.02.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 02/02/2017] [Accepted: 02/15/2017] [Indexed: 12/13/2022]
Abstract
Strain KHD7T, a Gram-stain-positive rod-shaped, non-sporulating, strictly anaerobic bacterium, was isolated from the vaginal swab of a woman with bacterial vaginosis. We studied its phenotypic characteristics and sequenced its complete genome. The major fatty acids were C16:0 (44%), C18:2n6 (22%), and C18:1n9 (14%). The 1,806,744 bp long genome exhibited 49.24% G+C content; 1549 protein-coding and 51 RNA genes. Strain KHD7T exhibited a 93.5% 16S rRNA similarity with Olsenella uli, the phylogenetically closest species in the family Coriobacteriaceae. Therefore, strain KHD7T is sufficiently distinct to represent a new genus, for which we propose the name Olegusella massiliensis gen. nov., sp. nov. The type strain is KHD7T.
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Affiliation(s)
- Khoudia Diop
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Awa Diop
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Florence Bretelle
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France; Department of Gynecology and Obstetrics, Gynépole, Marseille, Pr Boubli et D'Ercole, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, AMU, Aix-Marseille Université, France
| | - Frédéric Cadoret
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Caroline Michelle
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Magali Richez
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Jean-François Cocallemen
- Department of Gynecology and Obstetrics, Gynépole, Marseille, Pr Boubli et D'Ercole, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, AMU, Aix-Marseille Université, France
| | - Didier Raoult
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Florence Fenollar
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France.
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11
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Munson E, Carroll KC. What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015. J Clin Microbiol 2017; 55:24-42. [PMID: 27795334 PMCID: PMC5228236 DOI: 10.1128/jcm.01379-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.
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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, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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12
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Srinivasan S, Munch MM, Sizova MV, Fiedler TL, Kohler CM, Hoffman NG, Liu C, Agnew KJ, Marrazzo JM, Epstein SS, Fredricks DN. More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria. J Infect Dis 2016; 214 Suppl 1:S21-8. [PMID: 27449870 PMCID: PMC4957512 DOI: 10.1093/infdis/jiw192] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Women with bacterial vaginosis (BV) have complex communities of anaerobic bacteria. There are no cultivated isolates of several bacteria identified using molecular methods and associated with BV. It is unclear whether this is due to the inability to adequately propagate these bacteria or to correctly identify them in culture. METHODS Vaginal fluid from 15 women was plated on 6 different media using classical cultivation approaches. Individual isolates were identified by 16S ribosomal RNA (rRNA) gene sequencing and compared with validly described species. Bacterial community profiles in vaginal samples were determined using broad-range 16S rRNA gene polymerase chain reaction and pyrosequencing. RESULTS We isolated and identified 101 distinct bacterial strains spanning 6 phyla including (1) novel strains with <98% 16S rRNA sequence identity to validly described species, (2) closely related species within a genus, (3) bacteria previously isolated from body sites other than the vagina, and (4) known bacteria formerly isolated from the vagina. Pyrosequencing showed that novel strains Peptoniphilaceae DNF01163 and Prevotellaceae DNF00733 were prevalent in women with BV. CONCLUSIONS We isolated a diverse set of novel and clinically significant anaerobes from the human vagina using conventional approaches with systematic molecular identification. Several previously "uncultivated" bacteria are amenable to conventional cultivation.
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MESH Headings
- Bacteria, Anaerobic/classification
- Bacteria, Anaerobic/cytology
- Bacteria, Anaerobic/genetics
- Bacteria, Anaerobic/isolation & purification
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Female
- Gardnerella vaginalis/classification
- Gardnerella vaginalis/cytology
- Gardnerella vaginalis/genetics
- Gardnerella vaginalis/isolation & purification
- Humans
- Microbiota
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Vagina/microbiology
- Vaginosis, Bacterial/microbiology
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Affiliation(s)
- Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Matthew M Munch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Maria V Sizova
- Department of Biology, Northeastern University, Boston, Massachusetts
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Christina M Kohler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | | | - Congzhou Liu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | | | | | - Slava S Epstein
- Department of Biology, Northeastern University, Boston, Massachusetts
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center Department of Medicine Department of Microbiology, University of Washington, Seattle
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13
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Cools P, Ho E, Vranckx K, Schelstraete P, Wurth B, Franckx H, Ieven G, Van Simaey L, Van Daele S, Verhulst S, De Baets F, Vaneechoutte M. Epidemic Achromobacter xylosoxidans strain among Belgian cystic fibrosis patients and review of literature. BMC Microbiol 2016; 16:122. [PMID: 27342812 PMCID: PMC4919866 DOI: 10.1186/s12866-016-0736-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 06/08/2016] [Indexed: 12/11/2022] Open
Abstract
Background Achromobacter xylosoxidans is increasingly being recognized as an emerging pathogen in cystic fibrosis. Recent severe infections with A. xylosoxidans in some of our cystic fibrosis (CF) patients led to a re-evaluation of the epidemiology of CF-associated A. xylosoxidans infections in two Belgian reference centres (Antwerp and Ghent). Several of these patients also stayed at the Rehabilitation Centre De Haan (RHC). In total, 59 A. xylosoxidans isolates from 31 patients (including 26 CF patients), collected between 2001 and 2014, were studied. We evaluated Matrix Assisted Laser Desorption Ionisation -Time of Flight mass spectrometry (MALDI-TOF) as an alternative for McRAPD typing. Results Both typing approaches established the presence of a major cluster, comprising isolates, all from 21 CF patients, including from two patients sampled when staying at the RHC a decade ago. This major cluster was the same as the cluster established already a decade ago at the RHC. A minor cluster consisted of 13 isolates from miscellaneous origin. A further seven isolates, including one from a non-CF patient who had stayed recently at the RHC, were singletons. Conclusions Typing results of both methods were similar, indicating transmission of a single clone of A. xylosoxidans among several CF patients from at least two reference centres. Isolates of the same clone were already observed at the RHC, a decade ago. It is difficult to establish to what extent the RHC is the source of transmission, because the epidemic strain was already present when the first epidemiological study in the RHC was carried out. This study also documents the applicability of MALDI-TOF for typing of strains within the species A. xylosoxidans and the need to use the dynamic cutoff algorithm of the BioNumerics® software for correct clustering of the fingerprints. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0736-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Piet Cools
- Laboratory Bacteriology Research (LBR), Department of Microbiology, Immunology, and Clinical Chemistry, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
| | - Erwin Ho
- Cystic Fibrosis Centre, Antwerp University Hospital (AUH), Antwerp, Belgium
| | | | | | - Bettina Wurth
- Zeepreventorium (Rehabilitation Centre, RHC), De Haan, Belgium
| | - Hilde Franckx
- Zeepreventorium (Rehabilitation Centre, RHC), De Haan, Belgium
| | - Greet Ieven
- Department of Microbiology, Antwerp University Hospital, Antwerp, Belgium
| | - Leen Van Simaey
- Laboratory Bacteriology Research (LBR), Department of Microbiology, Immunology, and Clinical Chemistry, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
| | - Sabine Van Daele
- Cystic Fibrosis Centre, Ghent University Hospital (GUH), Ghent, Belgium
| | - Stijn Verhulst
- Cystic Fibrosis Centre, Antwerp University Hospital (AUH), Antwerp, Belgium
| | - Frans De Baets
- Cystic Fibrosis Centre, Ghent University Hospital (GUH), Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research (LBR), Department of Microbiology, Immunology, and Clinical Chemistry, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.
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Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2013-2014. Diagn Microbiol Infect Dis 2015; 83:82-8. [PMID: 26014276 DOI: 10.1016/j.diagmicrobio.2015.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 04/28/2015] [Indexed: 12/21/2022]
Abstract
A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate and rapid reporting and communications regarding infectious agents of clinical significance. Microbial taxonomy in the age of molecular diagnostics and phylogenetics causes changes in this taxonomy at a rapid rate further complicating this process. This review focuses on the description of new species and classification changes proposed over the past 2 years.
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