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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: 123] [Impact Index Per Article: 30.8] [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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Infección por Oerskovia turbata. Med Clin (Barc) 2020; 155:135-136. [DOI: 10.1016/j.medcli.2019.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/29/2019] [Accepted: 05/02/2019] [Indexed: 11/20/2022]
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Rohowetz LJ, Patel NA, Yannuzzi NA, Fan KC, Miller D, Flynn Jr. HW. Post-Traumatic Endophthalmitis Caused by <b><i>Oerskovia turbata</i></b>. Case Rep Ophthalmol 2019; 10:312-318. [PMID: 31607896 PMCID: PMC6787431 DOI: 10.1159/000502413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 07/30/2019] [Indexed: 11/19/2022] Open
Abstract
Purpose To present a previously unreported cause of bacterial endophthalmitis manifesting as delayed post-traumatic endophthalmitis ultimately responsive to total capsulectomy. Case Report A patient presented with chronic endophthalmitis that occurred after ocular trauma with organic material and Oerskovia turbata was eventually isolated. After a prolonged treatment course, including two pars plana vitrectomies and total capsulectomy, the patient achieved 20/80 visual acuity at 1-year follow-up. Conclusion This is the first reported patient with endophthalmitis due to O. turbata, a Gram-positive bacillus found in soil that rarely causes human infection. The infection had a delayed presentation despite early prophylactic antibiotics and was ultimately eliminated with total capsulectomy. Removal of lens and lens capsule may be necessary in the management of post-traumatic endophthalmitis unresponsive to more conservative therapy, particularly in cases involving atypical organisms and lens capsule violation.
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Affiliation(s)
- Landon J. Rohowetz
- University of Missouri – Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Nimesh A. Patel
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, Florida, USA
| | - Nicolas A. Yannuzzi
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, Florida, USA
| | - Kenneth C. Fan
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, Florida, USA
| | - Darlene Miller
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, Florida, USA
| | - Harry W. Flynn Jr.
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miami, Florida, USA
- *Harry W. Flynn Jr., Department of Ophthalmology, Bascom Palmer Eye Institute, 900 NW 17th St., Miami, FL 33136 (USA), E-Mail
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Suss PH, Ribeiro VST, Cieslinski J, Kraft L, Tuon FF. Experimental procedures for decontamination and microbiological testing in cardiovascular tissue banks. Exp Biol Med (Maywood) 2019; 243:1286-1301. [PMID: 30614255 DOI: 10.1177/1535370218820515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
IMPACT STATEMENT Sterility testing is a critical issue in the recovery, processing, and release of tissue allografts. Contaminated allografts are often discarded, increasing costs, and reducing tissue stocks. Given these concerns, it is important to determine the most effective methodology for sterility testing. This work provides an overview of microbiological methods for sampling and culturing donor grafts for cardiovascular tissue banking.
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Affiliation(s)
- Paula Hansen Suss
- 1 Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR 80215-901, Brazil
| | - Victoria Stadler Tasca Ribeiro
- 1 Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR 80215-901, Brazil
| | - Juliette Cieslinski
- 1 Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR 80215-901, Brazil
| | - Letícia Kraft
- 1 Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR 80215-901, Brazil
| | - Felipe Francisco Tuon
- 1 Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR 80215-901, Brazil.,2 Human Tissue Bank, Pontifícia Universidade Católica do Paraná, Curitiba, PR 80215-901, Brazil
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Species of family Promicromonosporaceae and family Cellulomonadeceae that produce cellulosome-like multiprotein complexes. Biotechnol Lett 2017; 40:335-341. [PMID: 29204770 DOI: 10.1007/s10529-017-2469-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/31/2017] [Indexed: 10/18/2022]
Abstract
OBJECTIVES To screen the phylogenetically-nearest members of Cellulosimicrobium cellulans for the production of cellulosome-like multienzyme complexes and extracellular β-xylosidase activity against 7-xylosyltaxanes and to get corresponding molecular insights. RESULTS Cellulosimicrobium (family Promicromonosporaceae) and all genera of the family Cellulomonadeceaec produced both cellulosome-like multienzyme complexes and extracellular β-xylosidase activity, while the other genera of the family Promicromonosporaceae did not. Multiple sequence alignments further indicated that hypothetic protein M768_06655 might be a possible key subunit. CONCLUSION This is the first report that many actinobacteria species can produce cellulosome-like multienzyme complexes. The production of cellulosome-like complexes and the extracellular β-xylosidase activity against 7-xylosyltaxanes might be used to differentiate the genus Cellulosimicrobium from other genera of the family Promicromonosporaceae.
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Dou TY, Luan HW, Liu XB, Li SY, Du XF, Yang L. Enzymatic hydrolysis of 7-xylosyltaxanes by an extracellular xylosidase from Cellulosimicrobium cellulans. Biotechnol Lett 2015; 37:1905-10. [PMID: 26026963 DOI: 10.1007/s10529-015-1867-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVES To find extracellular biocatalysts that can specifically and efficiently remove the C-7 xylosyl group from 7-xylosyltaxanes. RESULTS A Cellulosimicrobium cellulans strain F16 that can remove the C-7 xylosyl group from 7-xylosyltaxanes was isolated from the root soil of an old Taxus yunnanensis tree. Using corn cob as sole carbon source, the maximum 7-xylosyl-10-deacetylpaclitaxel β-xylosidase activity of 9.6 U l(-1) was achieved. The β-xylosidase could be trapped by a ceramic tubular membrane (pore size 50 nm), and exhibited an apparent molecular weight much greater than 500 kDa. Under optimized conditions, 3.75 l cell-free culture medium transformed 2 grams 7-xylosyltaxane mixtures to their corresponding aglycones within 3 h, with a conversion >98%. CONCLUSION This is the first report that C. cellulans can produce extracellular β-xylosidases capable of removing the C-7 xylosyl group from 7-xylosyltaxanes.
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Affiliation(s)
- Tong-Yi Dou
- Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457, Zhongshan Road, Dalian, 116023, Liaoning, People's Republic of China
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Abstract
Cellulosimicrobium cellulans has been reported as a rare cause of human pathogenesis. Infections mainly occur in immunocompromised patients and very often are associated with a foreign body. We report the first case of septic arthritis caused by C. cellulans in an immunocompetent patient. Our patient suffered a penetrating palm tree thorn injury to his left knee 8 weeks before admission. Although no foreign objects were found, they were suspected because previous reports suggest a frequent association with this microorganism, and open debridament was performed. Removal of foreign bodies related to this organism must be considered a high-priority treatment in these patients to achieve a complete recovery.
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Cellulosimicrobium funkei: first report of infection in a nonimmunocompromised patient and useful phenotypic tests for differentiation from Cellulosimicrobium cellulans and Cellulosimicrobium terreum. J Clin Microbiol 2011; 49:1175-8. [PMID: 21227990 DOI: 10.1128/jcm.01103-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cellulosimicrobium funkei is a rare, opportunistic pathogen. We describe a case of bacteremia and possibly prosthetic valve endocarditis by this organism in a nonimmunocompromised patient. Useful phenotypic tests for differentiating C. funkei from Cellulosimicrobium cellulans and Cellulosimicrobium terreum include motility, raffinose fermentation, glycogen, D-xylose, and methyl-α-D-glucopyranoside assimilation, and growth at 35°C.
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First report of acute cholecystitis with sepsis caused by Cellulomonas denverensis. J Clin Microbiol 2009; 47:3391-3. [PMID: 19656981 DOI: 10.1128/jcm.00678-09] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cellulomonas denverensis is a small and thin gram-positive rod-shaped bacterium that was proposed as a new species in 2005. Here we report a female case of acute cholecystitis and sepsis in which C. denverensis was determined to be causative.
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Brown JM, Steigerwalt AG, Morey RE, Daneshvar MI, Romero LJ, McNeil MM. Characterization of clinical isolates previously identified as Oerskovia turbata: proposal of Cellulosimicrobium funkei sp. nov. and emended description of the genus Cellulosimicrobium. Int J Syst Evol Microbiol 2006; 56:801-804. [PMID: 16585698 DOI: 10.1099/ijs.0.63882-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Taxonomic studies were performed on 13 clinical isolates (ten of which were epidemiologically related) that had been previously identified as Oerskovia turbata. Comparative phylogenetic analysis, based on 16S rRNA gene sequences, indicated that the isolates are closely related to Cellulosimicrobium cellulans with sequence similarity values ranging from 99.5 to 99.8 %. Chemotaxonomic results (fatty acid profiles and menaquinones) supported the inclusion of these isolates in the genus Cellulosimicrobium. The DNA G+C content was 74.5 mol%. The results of DNA-DNA reassociation, whole-cell sugars (with galactose as the characteristic whole sugar) and phenotypic properties, including antimicrobial resistance, indicated that these isolates are representatives of a novel species of the genus Cellulosimicrobium. The name Cellulosimicrobium funkei sp. nov. is proposed for the novel strains, with strain W6122T (=ATCC BAA-886T = DSM 16025T = CCUG 50705T) as the type strain. The definition of this novel Cellulosimicrobium species will assist in the understanding of the epidemiology and clinical significance of these micro-organisms.
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Affiliation(s)
- June M Brown
- Meningitis and Special Pathogens Branch; Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Arnold G Steigerwalt
- Meningitis and Special Pathogens Branch; Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Roger E Morey
- Meningitis and Special Pathogens Branch; Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Maryam I Daneshvar
- Meningitis and Special Pathogens Branch; Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Leslie-Joy Romero
- Meningitis and Special Pathogens Branch; Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Michael M McNeil
- Meningitis and Special Pathogens Branch; Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Rowlinson MC, Bruckner DA, Hinnebusch C, Nielsen K, Deville JG. Clearance of Cellulosimicrobium cellulans bacteremia in a child without central venous catheter removal. J Clin Microbiol 2006; 44:2650-4. [PMID: 16825406 PMCID: PMC1489490 DOI: 10.1128/jcm.02485-05] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Cellulosimicrobium cellulans (formerly known as Oerskovia xanthineolytica) rarely causes human infection. Infections have been reported in immunocompromised hosts or in patients with foreign bodies, such as catheters, where treatment has generally involved removal of the foreign body. We report on a case in which the organism was isolated in multiple blood cultures from a 13-year-old male. After initial therapy failed, treatment with vancomycin and rifampin resulted in infection clearance without removal of the central venous catheter.
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Affiliation(s)
- Marie-Claire Rowlinson
- UCLA School of Medicine, Department of Pathology and Laboratory Medicine, 10833 LeConte Avenue, Los Angeles, CA 90095-1752, USA
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Verma P, Brown JM, Nunez VH, Morey RE, Steigerwalt AG, Pellegrini GJ, Kessler HA. Native valve endocarditis due to Gordonia polyisoprenivorans: case report and review of literature of bloodstream infections caused by Gordonia species. J Clin Microbiol 2006; 44:1905-8. [PMID: 16672437 PMCID: PMC1479208 DOI: 10.1128/jcm.44.5.1905-1908.2006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the first case of endocarditis caused by Gordonia polyisoprenivorans and concisely review the English literature regarding bloodstream infections caused by Gordonia species.
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Affiliation(s)
- Punam Verma
- Division of Clinical Microbiology, Department of Pathology, Rush Medical College, Rush University Medical Center, Chicago, Illinois 60612, USA.
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Brown JM, Frazier RP, Morey RE, Steigerwalt AG, Pellegrini GJ, Daneshvar MI, Hollis DG, McNeil MM. Phenotypic and genetic characterization of clinical isolates of CDC coryneform group A-3: proposal of a new species of Cellulomonas, Cellulomonas denverensis sp. nov. J Clin Microbiol 2005; 43:1732-7. [PMID: 15814993 PMCID: PMC1081325 DOI: 10.1128/jcm.43.4.1732-1737.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CDC coryneform group A-3 bacteria are rare human pathogens. In this study, six group A-3 isolates (two from blood, one from cerebrospinal fluid, and one each from homograft valve, lip wound, and pilonidal cyst) were compared to the type strains of phenotypically related organisms, Cellulomonas fimi, Cellulomonas hominis, Oerskovia turbata, and Sanguibacter suarezii, and characterized by phenotypic, chemotaxonomic, and genotypic studies. DNA-DNA reassociation analysis identified two genomic groups, and phylogenetic analysis of the 16S rRNA gene sequence identified the taxonomic positions of these groups to genus level. Two groups were defined, and both were more closely related to Cellulomonas species: one group of three strains, for which we propose the new species Cellulomonas denverensis sp. nov., with the type strain W6929 (ATCC BAA-788(T) or DSM 15764(T)), was related to C. hominis ATCC 51964(T) (98.5% 16S rRNA gene sequence similarity), and the second group of three strains was related to C. hominis ATCC 51964(T) (99.8 to 99.9% 16S rRNA gene sequence similarity). The definition of this new Cellulomonas species and the confirmation of three strains as C. hominis serve to further clarify the complex taxonomy of CDC coryneform group A-3 bacteria and will assist in our understanding of the epidemiology and clinical significance of these microorganisms.
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Affiliation(s)
- June M Brown
- Meningitis and Special Pathogens Branch, Centers for Disease Control and Prevention, Bldg. 17-2207, Mailstop G-34, Atlanta, GA 30333, USA.
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Corynebacterium species and coryneforms: An update on taxonomy and diseases attributed to these taxa. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.clinmicnews.2005.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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