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Fida M, Wolf MJ, Hamdi A, Vijayvargiya P, Esquer Garrigos Z, Khalil S, Greenwood-Quaintance KE, Thoendel MJ, Patel R. Detection of Pathogenic Bacteria From Septic Patients Using 16S Ribosomal RNA Gene-Targeted Metagenomic Sequencing. Clin Infect Dis 2021; 73:1165-1172. [PMID: 33893492 PMCID: PMC8492209 DOI: 10.1093/cid/ciab349] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Conventional blood cultures were compared to plasma cell-free DNA-based 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR)/next-generation sequencing (NGS) for detection and identification of potential pathogens in patients with sepsis. METHODS Plasma was prospectively collected from 60 adult patients with sepsis presenting to the Mayo Clinic (Minnesota) Emergency Department from March through August 2019. Results of routine clinical blood cultures were compared to those of 16S rRNA gene NGS. RESULTS Nineteen (32%) subjects had positive blood cultures, of which 13 yielded gram-negative bacilli, 5 gram-positive cocci, and 1 both gram-negative bacilli and gram-positive cocci. 16S rRNA gene NGS findings were concordant in 11. For the remaining 8, 16S rRNA gene NGS results yielded discordant detections (n = 5) or were negative (n = 3). Interestingly, Clostridium species were additionally detected by 16S rRNA gene NGS in 3 of the 6 subjects with gastrointestinal sources of gram-negative bacteremia and none of the 3 subjects with urinary sources of gram-negative bacteremia. In the 41 remaining subjects, 16S rRNA gene NGS detected at least 1 potentially pathogenic organism in 17. In 15, the detected microorganism clinically correlated with the patient's syndrome. In 17 subjects with a clinically defined infectious syndrome, neither test was positive; in the remaining 7 subjects, a noninfectious cause of clinical presentation was identified. CONCLUSIONS 16S rRNA gene NGS may be useful for detecting bacteria in plasma of septic patients. In some cases of gram-negative sepsis, it may be possible to pinpoint a gastrointestinal or urinary source of sepsis based on the profile of bacteria detected in plasma.
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Affiliation(s)
- Madiha Fida
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew J Wolf
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ahmed Hamdi
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Prakhar Vijayvargiya
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississipi, USA
| | - Zerelda Esquer Garrigos
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississipi, USA
| | - Sarwat Khalil
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Matthew J Thoendel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
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Molecular Basis for the Activation of Human Innate Immune Response by the Flagellin Derived from Plant-Pathogenic Bacterium, Acidovorax avenae. Int J Mol Sci 2021; 22:ijms22136920. [PMID: 34203170 PMCID: PMC8268093 DOI: 10.3390/ijms22136920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/15/2022] Open
Abstract
Acidovorax avenae is a flagellated, pathogenic bacterium to various plant crops that has also been found in human patients with haematological malignancy, fever, and sepsis; however, the exact mechanism for infection in humans is not known. We hypothesized that the human innate immune system could be responsive to the purified flagellin isolated from A. avenae, named FLA-AA. We observed the secretion of inflammatory cytokines such as tumor necrosis factor-alpha (TNF-α), interleukin (IL)-6, and IL-8 by treating FLA-AA to human dermal fibroblasts, as well as macrophages. This response was exclusively through TLR5, which was confirmed by using TLR5-overexpression cell line, 293/hTLR5, as well as TLR5-specific inhibitor, TH1020. We also observed the secretion of inflammatory cytokine, IL-1β, by the activation of NLRC4 with FLA-AA. Overall, our results provide a molecular basis for the inflammatory response caused by FLA-AA in cell-based assays.
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Doulgeraki AI, Bikouli V, Argyri AA, Chorianopoulos N, Mitre E, Charvourou G, Sourri P, Tassou CC, Oikonomou A. Exploring the Bacterial Communities of the Kaiafas Thermal Spring Anigrides Nymphes in Greece Prior to Rehabilitation Actions. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E9133. [PMID: 33297492 PMCID: PMC7730472 DOI: 10.3390/ijerph17239133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/30/2020] [Accepted: 12/05/2020] [Indexed: 11/16/2022]
Abstract
Anigrides Nymphes of Lake Kaiafas is a thermal spring that is well known for its therapeutical properties, as the hot water (32-34 °C) is rich in sulfur compounds and minerals. Nowadays, efforts are made from the Hellenic Republic to modernize the existing facilities and infrastructure networks of the area. To study the complex ecosystem of the thermal spring, we collected water from four sampling points (Lake, and Caves 1, 2, and 3). Filtration method was used for microbial enumeration. In parallel, total bacterial DNA was extracted and subjected to next-generation sequencing (NGS). A total of 166 different bacterial families were detected. Differences in families, genera, and species abundances were detected between the different sampling points. Specifically, Comamonadaceae was the most common family detected in Lake and Cave 3. Similarly, in Caves 1 and 2, Rhodobacteraceae was detected at a higher percentage compared to the rest of the families. Moreover, the detection of sequences assigned to waterborne or opportunistic pathogens, i.e., Enterobacteriaceae, Legionellaceae, Coxiellaceae, and Clostridiaceae, as well as Enterococcus and Vibrio, is of great importance. Although the presence of pathogens was not examined by quantitative PCR, the detection of their sequences strengthens the need of the planned rehabilitation actions of this natural environment in order to allow human swimming.
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Affiliation(s)
- Agapi I. Doulgeraki
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, Sof. Venizelou 1, 14123 Lycovrissi, Greece; (V.B.); (A.A.A.); (N.C.); (E.M.); (G.C.); (P.S.); (C.C.T.)
| | - Vasiliki Bikouli
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, Sof. Venizelou 1, 14123 Lycovrissi, Greece; (V.B.); (A.A.A.); (N.C.); (E.M.); (G.C.); (P.S.); (C.C.T.)
| | - Anthoula A. Argyri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, Sof. Venizelou 1, 14123 Lycovrissi, Greece; (V.B.); (A.A.A.); (N.C.); (E.M.); (G.C.); (P.S.); (C.C.T.)
| | - Nikos Chorianopoulos
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, Sof. Venizelou 1, 14123 Lycovrissi, Greece; (V.B.); (A.A.A.); (N.C.); (E.M.); (G.C.); (P.S.); (C.C.T.)
| | - Elisavet Mitre
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, Sof. Venizelou 1, 14123 Lycovrissi, Greece; (V.B.); (A.A.A.); (N.C.); (E.M.); (G.C.); (P.S.); (C.C.T.)
| | - Georgia Charvourou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, Sof. Venizelou 1, 14123 Lycovrissi, Greece; (V.B.); (A.A.A.); (N.C.); (E.M.); (G.C.); (P.S.); (C.C.T.)
| | - Patra Sourri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, Sof. Venizelou 1, 14123 Lycovrissi, Greece; (V.B.); (A.A.A.); (N.C.); (E.M.); (G.C.); (P.S.); (C.C.T.)
| | - Chrysoula C. Tassou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, Sof. Venizelou 1, 14123 Lycovrissi, Greece; (V.B.); (A.A.A.); (N.C.); (E.M.); (G.C.); (P.S.); (C.C.T.)
| | - Alexandra Oikonomou
- Ephorate of Palaeoanthropology and Speleology, Hellenic Republic Ministry of Culture and Sports, Ardittou 34b, 11636 Athens, Greece;
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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Hamner S, Brown BL, Hasan NA, Franklin MJ, Doyle J, Eggers MJ, Colwell RR, Ford TE. Metagenomic Profiling of Microbial Pathogens in the Little Bighorn River, Montana. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16071097. [PMID: 30934749 PMCID: PMC6479903 DOI: 10.3390/ijerph16071097] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/21/2019] [Accepted: 03/22/2019] [Indexed: 12/26/2022]
Abstract
The Little Bighorn River is the primary source of water for water treatment plants serving the local Crow Agency population, and has special significance in the spiritual and ceremonial life of the Crow tribe. Unfortunately, the watershed suffers from impaired water quality, with high counts of fecal coliform bacteria routinely measured during run-off events. A metagenomic analysis was carried out to identify potential pathogens in the river water. The Oxford Nanopore MinION platform was used to sequence DNA in near real time to identify both uncultured and a coliform-enriched culture of microbes collected from a popular summer swimming area of the Little Bighorn River. Sequences were analyzed using CosmosID bioinformatics and, in agreement with previous studies, enterohemorrhagic and enteropathogenic Escherichia coli and other E. coli pathotypes were identified. Noteworthy was detection and identification of enteroaggregative E. coli O104:H4 and Vibrio cholerae serotype O1 El Tor, however, cholera toxin genes were not identified. Other pathogenic microbes, as well as virulence genes and antimicrobial resistance markers, were also identified and characterized by metagenomic analyses. It is concluded that metagenomics provides a useful and potentially routine tool for identifying in an in-depth manner microbial contamination of waterways and, thereby, protecting public health.
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Affiliation(s)
- Steve Hamner
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA 2 Department of Microbiology, Montana State University, Bozeman, MT 59717, USA.
- Department of Microbiology, Montana State University, Bozeman, MT 59717, USA.
| | - Bonnie L Brown
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA.
| | - Nur A Hasan
- CosmosID Inc., 1600 East Gude Drive, Rockville, MD 20850, USA.
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.
| | - Michael J Franklin
- Department of Microbiology, Montana State University, Bozeman, MT 59717, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA.
| | - John Doyle
- Crow Water Quality Project, Crow Agency, Little Big Horn College, MT 59022, USA.
- Crow Environmental Health Steering Committee, Crow Agency, Little Big Horn College, MT 59022, USA.
| | - Margaret J Eggers
- Department of Microbiology, Montana State University, Bozeman, MT 59717, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA.
- Crow Environmental Health Steering Committee, Crow Agency, Little Big Horn College, MT 59022, USA.
| | - Rita R Colwell
- CosmosID Inc., 1600 East Gude Drive, Rockville, MD 20850, USA.
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.
| | - Timothy E Ford
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA 2 Department of Microbiology, Montana State University, Bozeman, MT 59717, USA.
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Hilton SK, Castro-Nallar E, Pérez-Losada M, Toma I, McCaffrey TA, Hoffman EP, Siegel MO, Simon GL, Johnson WE, Crandall KA. Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology. Front Microbiol 2016; 7:484. [PMID: 27092134 PMCID: PMC4823605 DOI: 10.3389/fmicb.2016.00484] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/22/2016] [Indexed: 12/12/2022] Open
Abstract
Diagnoses that are both timely and accurate are critically important for patients with life-threatening or drug resistant infections. Technological improvements in High-Throughput Sequencing (HTS) have led to its use in pathogen detection and its application in clinical diagnoses of infectious diseases. The present study compares two HTS methods, 16S rRNA marker gene sequencing (metataxonomics) and whole metagenomic shotgun sequencing (metagenomics), in their respective abilities to match the same diagnosis as traditional culture methods (culture inference) for patients with ventilator associated pneumonia (VAP). The metagenomic analysis was able to produce the same diagnosis as culture methods at the species-level for five of the six samples, while the metataxonomic analysis was only able to produce results with the same species-level identification as culture for two of the six samples. These results indicate that metagenomic analyses have the accuracy needed for a clinical diagnostic tool, but full integration in diagnostic protocols is contingent on technological improvements to decrease turnaround time and lower costs.
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Affiliation(s)
- Sarah K Hilton
- Computational Biology Institute, The George Washington University Ashburn, VA, USA
| | - Eduardo Castro-Nallar
- Computational Biology Institute, The George Washington UniversityAshburn, VA, USA; Facultad de Ciencias Biológicas, Center for Bioinformatics and Integrative Biology, Universidad Andres BelloSantiago, Chile
| | - Marcos Pérez-Losada
- Computational Biology Institute, The George Washington UniversityAshburn, VA, USA; Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO)Vairão, Portugal; Children's National Medical Research CenterWashington DC, USA
| | - Ian Toma
- Division of Genomic Medicine, Department of Medicine, The George Washington University School of Medicine and Health Sciences Washington DC, USA
| | - Timothy A McCaffrey
- Division of Genomic Medicine, Department of Medicine, Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University School of Medicine and Health Sciences Washington DC, USA
| | - Eric P Hoffman
- Children's National Medical Research Center Washington DC, USA
| | - Marc O Siegel
- Division of Infectious Diseases, Department of Medicine, School of Medicine and Health Sciences, The George Washington University Washington DC, USA
| | - Gary L Simon
- Division of Infectious Diseases, Department of Medicine, School of Medicine and Health Sciences, The George Washington University Washington DC, USA
| | - W Evan Johnson
- Computational Biomedicine, Boston University School of Medicine Boston, MA, USA
| | - Keith A Crandall
- Computational Biology Institute, The George Washington University Ashburn, VA, USA
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First Draft Genome Sequence of the Acidovorax caeni sp. nov. Type Strain R-24608 (DSM 19327). GENOME ANNOUNCEMENTS 2015; 3:3/6/e01378-15. [PMID: 26586902 PMCID: PMC4653804 DOI: 10.1128/genomea.01378-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the draft genome sequence of the Acidovorax caeni type strain R-24608 that was isolated from activated sludge of an aerobic-anaerobic wastewater treatment plant. The closest strain to Acidovorax caeni strain R-24608 is Acidovorax sp. strain MR-S7 with a 55.4% (amino-acid sequence) open reading frames (ORFs) average similarity.
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8
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Abstract
Acidovorax oryzae is a bacterium that has never before been reported as pathogenic in human subjects. Here we describe the first case of a successfully treated A. oryzae catheter-associated bloodstream infection in an immunocompetent patient prior to heart transplantation.
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Davenport AC, Mascarelli PE, Maggi RG, Breitschwerdt EB. Phylogenetic diversity of bacteria isolated from sick dogs using the BAPGM enrichment culture platform. J Vet Intern Med 2013; 27:854-61. [PMID: 23647339 DOI: 10.1111/jvim.12094] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 02/19/2013] [Accepted: 03/13/2013] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Bartonella alpha-Proteobacteria growth medium (BAPGM) enrichment culture has proven useful for documenting Bartonella species infection and has facilitated growth of other fastidious bacteria from human samples. PURPOSE To report non-Bartonella bacterial isolates obtained from canine samples cultured using BAPGM enrichment culture. ANIMALS Between 2004 and 2008, 695 specimens from 513 dogs were tested by the NCSU-IPRL using the BAPGM enrichment culture. Over the same period of time, blood samples from 270 dogs were cultured by the NCSU-CML using Bactec-Plus Aerobic/F media. METHODS BAPGM isolates were characterized using Bartonella genus primers and 16S rDNA primers followed by DNA sequencing. NCSU medical records were retrospectively reviewed. Blood culture results from the NCSU-CML were compared with BAPGM blood culture results. RESULTS Seventy-nine non-Bartonella isolates were obtained from 69/513 dogs. The most commonly isolated phylum was Proteobacteria (48.1%) with alpha-Proteobacteria being the most commonly isolated class. Staphylococcus and Sphingomonas were the most commonly isolated genera. The majority of the remaining isolates were bacteria that are rarely isolated from canine samples. Comparison of NCSU-CML and IPRL (BAPGM) blood culture isolates showed alpha-Proteobacteria were isolated more often from BAPGM. CONCLUSIONS AND CLINICAL IMPORTANCE Use of insect cell culture enrichment medium, such as BAPGM, appears to enhance the growth of alpha-Proteobacteria, but also results in isolation of non-alpha-Proteobacteria from sick dogs. Future studies are needed to elucidate the utility of BAPGM and other "nonconventional" growth media and methods for isolation of fastidious organisms and to determine if these organisms play a causal role in disease development.
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Affiliation(s)
- A C Davenport
- Intracellular Pathogens Research Laboratory, Center for Comparative Medicine and Translational Research, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
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Vaneechoutte M, Janssens M, Avesani V, Delmée M, Deschaght P. Description of Acidovorax wautersii sp. nov. to accommodate clinical isolates and an environmental isolate, most closely related to Acidovorax avenae. Int J Syst Evol Microbiol 2012; 63:2203-2206. [PMID: 23148096 DOI: 10.1099/ijs.0.046102-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-negative strains, NF 1078(T), NF 1598 and NF 1715, were isolated from clinical (two) and environmental (one) samples, respectively. Sequence analysis of the 16S rRNA genes revealed similarity of 100% among the three strains and next highest similarity to the type strain of Acidovorax avenae (98.16%). The three strains were able to acidify lactose and rhamnose on low peptone phenol red agar and to alkalinize citrate on Simmons' agar and were negative for nitrate reduction. The DNA G+C content of strain NF 1078(T) was 67.1 mol%. The level of DNA-DNA relatedness between this strain and the type strains of A. avenae (ATCC 19860(T), LMG 2117(T)) was 29%. Based on these phylogenetic, phenotypic and genotypic analyses, the three strains could be distinguished clearly from all other recognized Acidovorax species and should be classified as representatives of a novel species of the genus Acidovorax, for which the name Acidovorax wautersii sp. nov. is proposed. The type strain is NF 1078(T) (=LMG 26971(T)=CCUG 62584(T)).
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Affiliation(s)
- Mario Vaneechoutte
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium
| | - Michèle Janssens
- Medical Microbiology, University of Louvain, UCL, Brussels, Belgium
| | | | - Michel Delmée
- Medical Microbiology, University of Louvain, UCL, Brussels, Belgium
| | - Pieter Deschaght
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium
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Implanted-port-catheter-related sepsis caused by Acidovorax avenae and methicillin-sensitive Staphylococcus aureus. J Clin Microbiol 2009; 47:3358-61. [PMID: 19710279 DOI: 10.1128/jcm.01093-09] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acidovorax avenae is a gram-negative rod in the family Comamonadaceae and a phytopathogen found in the environment. Human infections caused by members of the Comamonadaceae are extremely rare. We report a case of implanted-port-catheter-related sepsis caused by Acidovorax avenae and methicillin (meticillin)-sensitive Staphylococcus aureus (MSSA).
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12
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Larsen MKS, Thomsen TR, Moser C, Høiby N, Nielsen PH. Use of cultivation-dependent and -independent techniques to assess contamination of central venous catheters: a pilot study. BMC Clin Pathol 2008; 8:10. [PMID: 18954471 PMCID: PMC2605442 DOI: 10.1186/1472-6890-8-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Accepted: 10/28/2008] [Indexed: 02/08/2023] Open
Abstract
Background Catheters are the most common cause of nosocomial infections and are associated with increased risk of mortality, length of hospital stay and cost. Prevention of infections and fast and correct diagnosis is highly important. Methods In this study traditional semiquantitative culture-dependent methods for diagnosis of bacteria involved in central venous catheter-related infections as described by Maki were compared with the following culture-independent molecular biological methods: Clone libraries, denaturant gradient gel electrophoresis, phylogeny and fluorescence in situ hybridization. Results In accordance with previous studies, the cultivation of central venous catheters from 18 patients revealed that S. epidermidis and other coagulase-negative staphylococci were most abundant and that a few other microorganisms such as P. aeruginosa and K. pneumoniae occasionally were found on the catheters. The molecular analysis using clone libraries and sequencing, denaturant gradient gel electrophoresis and sequencing provided several important results. The species found by cultivation were confirmed by molecular methods. However, many other bacteria belonging to the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were also found, stressing that only a minor portion of the species present were found by cultivation. Some of these bacteria are known to be pathogens, some have not before been described in relation to human health, and some were not closely related to known pathogens and may represent new pathogenic species. Furthermore, there was a clear difference between the bacterial species found in biofilm on the external (exluminal) and internal (luminal) side of the central venous catheter, which can not be detected by Maki's method. Polymicrobial biofilms were observed on most of the catheters and were much more common than the cultivation-dependent methods indicated. Conclusion The results show that diagnosis based on molecular methods improves the detection of microorganisms involved in central catheter-related infections. The importance of these microorganisms needs to be investigated further, also in relation to contamination risk from improper catheter handling, as only in vivo contaminants are of interest. This information can be used for development of fast and more reliable diagnostic tools, which can be used in combination with traditional methods.
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Affiliation(s)
- Mette K S Larsen
- Department of Biotechnology, Chemistry, and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark.
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13
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Bacterial signatures in atherosclerotic lesions represent human commensals and pathogens. Atherosclerosis 2008; 201:192-7. [PMID: 18342318 DOI: 10.1016/j.atherosclerosis.2008.01.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 01/17/2008] [Accepted: 01/23/2008] [Indexed: 11/24/2022]
Abstract
BACKGROUND Various studies have suggested the involvement of infectious agents in chronic inflammatory diseases, including atherosclerosis. By using a novel subtraction broad-range PCR approach, we defined bacterial DNA signatures in surgically removed sterile abdominal aorta samples of patients with aortic atherosclerosis. METHODS Partial bacterial 16S rDNA nucleotide sequences were determined using broad-range PCR from aortic samples of 20 patients, and from appropriate methodological controls. In all, 160 sequences from 16 clone libraries were studied. RESULTS After subtraction analysis 16 clinically relevant bacterial sequence-types were identified among the patient samples, whereas 29 were discarded as potential methodological contaminants. On average 2.2+/-1.2 different bacterial sequence-types were present in the nine true PCR-positive atheroma samples. CONCLUSIONS Many studies have reported the presence of a variety of bacterial sequences from atherosclerotic lesions. However, the results obtained with these PCR technologies may have been skewed by methodological contaminants. After our subtraction approach, 63% of the remaining sequence-types from sites of aortic atherosclerosis were related to those of known human pathogens. This may imply that advanced atherosclerotic plaques accumulate bacterial DNA.
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