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Kopf A, Bunk B, Riedel T, Schröttner P. The zoonotic pathogen Wohlfahrtiimonas chitiniclastica - current findings from a clinical and genomic perspective. BMC Microbiol 2024; 24:3. [PMID: 38172653 PMCID: PMC10763324 DOI: 10.1186/s12866-023-03139-7] [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: 08/01/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
The zoonotic pathogen Wohlfahrtiimonas chitiniclastica can cause several diseases in humans, including sepsis and bacteremia. Although the pathogenesis is not fully understood, the bacterium is thought to enter traumatic skin lesions via fly larvae, resulting in severe myiasis and/or wound contamination. Infections are typically associated with, but not limited to, infestation of an open wound by fly larvae, poor sanitary conditions, cardiovascular disease, substance abuse, and osteomyelitis. W. chitiniclastica is generally sensitive to a broad spectrum of antibiotics with the exception of fosfomycin. However, increasing drug resistance has been observed and its development should be monitored with caution. In this review, we summarize the currently available knowledge and evaluate it from both a clinical and a genomic perspective.
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Affiliation(s)
- Anna Kopf
- Clinic for Cardiology, Sana Heart Center, Leipziger Str. 50, 03048, Cottbus, Germany
- 2nd Medical Clinic for Hematology, Oncology, Pneumology and Nephrology, Carl-Thiem Hospital Cottbus gGmbH, Cottbus, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Percy Schröttner
- Institute for Medical Microbiology and Virology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
- Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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Elgarahy AM, Al-Mur BA, Akhdhar A, El-Sadik HA, El-Liethy MA, Elwakeel KZ, Salama AM. Biosorption kinetics of cerium(III) and cobalt(II) from liquid wastes using individual bacterial species isolated from low-level liquid radioactive wastes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:15198-15216. [PMID: 36166126 DOI: 10.1007/s11356-022-23241-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
The existence of toxic heavy metals in the aquatic environment has emphasized a considerable exigency to develop several multifunctional biosorbents for their removal. Herein, three individual bacterial species of Cellulosimicrobium cellulans, Bacillus coagulans, and Microbacterium testaceum were successfully isolated from low-level liquid radioactive wastes. Their loading capacities towards cerium and cobalt metal ions were inclusivity inspected under variable operational parameters of pH, primary pollutant concentration, interaction time, temperature, stirring speed, and biosorbent dosage. By analyzing the influence of solution pH, concentration, temperature, biosorbent mass, and agitation speed on the biosorption kinetics, the biosorption process confirms pseudo-second-order kinetic, intraparticle diffusion, and Elovich equation. Remarkably, the isolated Microbacterium testaceum exhibited high loading capacities reaching 68.1 mg g-1, and 49.6 mg g-1 towards Ce(III), and Co(II) ions, respectively, at the initial concentration of 2.8 mM, pH 4.5, and 25 °C. Overall, the isolated bacterial species can potentially be offered up as a promising scavenger for Ce(III) and Co(II) from liquid waste effluents.
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Affiliation(s)
- Ahmed M Elgarahy
- Environmental Science Department, Faculty of Science, Port Said University, Port Said, Egypt
- Egyptian Propylene and Polypropylene Company (EPPC), Port Said, Egypt
| | - Bandar A Al-Mur
- Department of Environmental Science, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdullah Akhdhar
- Department of Chemistry, College of Science , University of Jeddah, Jeddah, Saudi Arabia
| | - Hamdy A El-Sadik
- Water Quality Audit Department, Egyptian Water and Wastewater Regulatory Agency (EWRA), New Cairo City, Egypt
- Hot Laboratories and Waste Management Centre, Atomic Energy Authority, Cairo, Egypt
| | - Mohamed Azab El-Liethy
- Environmental Microbiology Lab., Water Pollution Research Department, National Research Centre, Dokki, P.O. Box 12262., Giza, Egypt
| | - Khalid Z Elwakeel
- Environmental Science Department, Faculty of Science, Port Said University, Port Said, Egypt.
- Department of Chemistry, College of Science , University of Jeddah, Jeddah, Saudi Arabia.
| | - Abeer M Salama
- Environmental Science Department, Faculty of Science, Port Said University, Port Said, Egypt
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Ko HM, Jo JH, Baek HG. Effective Identification of Ochrobactrum anthropi Isolated from Clinical Specimens. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2020. [DOI: 10.15324/kjcls.2020.52.3.221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Hyun-Mi Ko
- Dental Science Research Institute, Department of Oral Anatomy, School of Dentistry, Chonnam National University, Gwangju, Korea
| | - Jun-Hyeon Jo
- Department of Laboratory Medicine, Kwangju Christian Hospital, Gwangju, Korea
| | - Hae-Gyeong Baek
- Department of Laboratory Medicine, Kwangju Christian Hospital, Gwangju, Korea
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Odogwu NM, Olayemi OO, Omigbodun AO. The vaginal microbiome of sub-Saharan African women: revealing important gaps in the era of next-generation sequencing. PeerJ 2020; 8:e9684. [PMID: 32879794 PMCID: PMC7441984 DOI: 10.7717/peerj.9684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/18/2020] [Indexed: 12/14/2022] Open
Abstract
Accurate characterization of the vaginal microbiome remains a fundamental goal of the Human Microbiome project (HMP). For over a decade, this goal has been made possible deploying high-throughput next generation sequencing technologies (NGS), which indeed has revolutionized medical research and enabled large-scale genomic studies. The 16S rRNA marker-gene survey is the most commonly explored approach for vaginal microbial community studies. With this approach, prior studies have elucidated substantial variations in the vaginal microbiome of women from different ethnicities. This review provides a comprehensive account of studies that have deployed this approach to describe the vaginal microbiota of African women in health and disease. On the basis of published data, the few studies reported from the African population are mainly in non-pregnant post pubertal women and calls for more detailed studies in pregnant and postnatal cohorts. We provide insight on the use of more sophisticated cutting-edge technologies in characterizing the vaginal microbiome. These technologies offer high-resolution detection of vaginal microbiome variations and community functional capabilities, which can shed light into several discrepancies observed in the vaginal microbiota of African women in an African population versus women of African descent in the diaspora.
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Affiliation(s)
- Nkechi Martina Odogwu
- Pan African University of Life and Earth Science Institute, Department of Obstetrics and Gynecology, University College Hospital, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Oladapo O. Olayemi
- Department of Obstetrics and Gynecology, College of Medicine, University College Hospital, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Akinyinka O. Omigbodun
- Department of Obstetrics and Gynecology, College of Medicine, University College Hospital, University of Ibadan, Ibadan, Oyo, Nigeria
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Rodenbaugh C, Ramachandran A, Brandão J. Lancefield Group A Streptococcus-Associated Dermatitis in an African Pygmy Hedgehog (Atelerix albiventris). J Exot Pet Med 2020. [DOI: 10.1053/j.jepm.2020.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kim HJ, Jun JW, Giri SS, Chi C, Yun S, Kim SG, Kim SW, Han SJ, Kwon J, Oh WT, Lee SB, Kim JH, Park SC. Identification and Genome Analysis of Vibrio coralliilyticus Causing Mortality of Pacific Oyster ( Crassostrea gigas) Larvae. Pathogens 2020; 9:E206. [PMID: 32168754 PMCID: PMC7157721 DOI: 10.3390/pathogens9030206] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/08/2020] [Accepted: 03/09/2020] [Indexed: 01/23/2023] Open
Abstract
Vibrio coralliilyticus is known as a coral pathogen that also infects marine bivalve larvae worldwide. It is considered to be one of the major constraints in artificial marine bivalve seed production as it causes mortality. In this study, we first isolated and characterized a high virulent of V. coralliilyticus designated as SNUTY-1 that was the cause of Pacific oyster larvae mortality in Korea. In the pathogenicity test, exposure to 2.14 × 105 CFU/mL for 24 h caused mortality to 88.65 ± 2.4% of the tested healthy Pacific oyster larvae. SNUTY-1 showed anti-microbial resistance to β-lactams, such as penicillins, cephalosporins, and carbapenems. We sequenced and assembled the complete genome of SNUTY-1 (5,842,676 bp), consisting of two chromosomes (Chr I and Chr II) and two plasmids (pSNUTY1 and pSNUTY2). The COG functional analysis confirmed that Chr I had more genes associated with basic cellular functions in comparison to Chr II. The results of the phylogenetic trees based on OrthoANI values indicated that the SNUTY-1 was closely related to V. coralliilyticus strains. SNUTY-1 had a unique plasmid (pSNUTY2), which could mean that the Korean isolate is different from other sequenced V. coralliilyticus strains from different geographical origins. Toxic proteins such as cytolysin/hemolysin and extracellular metalloprotease genes were encoded on Chr I and Chr II of SNUTY-1. These data facilitate the control of V. coralliilyticus infections in aquaculture by providing valuable insights into the biodiversity of this organism and valuable information for the study of virulence factors.
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Affiliation(s)
- Hyoun Joong Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (H.J.K.); (S.S.G.); (S.Y.); (S.G.K.); (S.W.K.); (S.J.H.); (J.K.); (W.T.O.); (S.B.L.)
| | - Jin Woo Jun
- Department of Aquaculture, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea;
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (H.J.K.); (S.S.G.); (S.Y.); (S.G.K.); (S.W.K.); (S.J.H.); (J.K.); (W.T.O.); (S.B.L.)
| | - Cheng Chi
- Laboratory of Aquatic Nutrition and Ecology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China;
| | - Saekil Yun
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (H.J.K.); (S.S.G.); (S.Y.); (S.G.K.); (S.W.K.); (S.J.H.); (J.K.); (W.T.O.); (S.B.L.)
| | - Sang Guen Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (H.J.K.); (S.S.G.); (S.Y.); (S.G.K.); (S.W.K.); (S.J.H.); (J.K.); (W.T.O.); (S.B.L.)
| | - Sang Wha Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (H.J.K.); (S.S.G.); (S.Y.); (S.G.K.); (S.W.K.); (S.J.H.); (J.K.); (W.T.O.); (S.B.L.)
| | - Se Jin Han
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (H.J.K.); (S.S.G.); (S.Y.); (S.G.K.); (S.W.K.); (S.J.H.); (J.K.); (W.T.O.); (S.B.L.)
| | - Jun Kwon
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (H.J.K.); (S.S.G.); (S.Y.); (S.G.K.); (S.W.K.); (S.J.H.); (J.K.); (W.T.O.); (S.B.L.)
| | - Woo Taek Oh
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (H.J.K.); (S.S.G.); (S.Y.); (S.G.K.); (S.W.K.); (S.J.H.); (J.K.); (W.T.O.); (S.B.L.)
| | - Sung Bin Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (H.J.K.); (S.S.G.); (S.Y.); (S.G.K.); (S.W.K.); (S.J.H.); (J.K.); (W.T.O.); (S.B.L.)
| | - Ji Hyung Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (H.J.K.); (S.S.G.); (S.Y.); (S.G.K.); (S.W.K.); (S.J.H.); (J.K.); (W.T.O.); (S.B.L.)
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Schumacher A, Vranken T, Malhotra A, Arts JJC, Habibovic P. In vitro antimicrobial susceptibility testing methods: agar dilution to 3D tissue-engineered models. Eur J Clin Microbiol Infect Dis 2018; 37:187-208. [PMID: 28871407 PMCID: PMC5780537 DOI: 10.1007/s10096-017-3089-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/20/2017] [Indexed: 12/22/2022]
Abstract
In the field of orthopaedic surgery, bacterial invasion of implants and the resulting periprosthetic infections are a common and unresolved problem. Antimicrobial susceptibility testing methods help to define the optimal treatment and identify antimicrobial resistance. This review discusses proven gold-standard techniques and recently developed models for antimicrobial susceptibility testing, while also providing a future outlook. Conventional, gold-standard methods, such as broth microdilution, are still widely applied in clinical settings. Although recently developed methods based on microfluidics and microdroplets have shown advantages over conventional methods in terms of testing speed, safety and the potential to provide a deeper insight into resistance mechanisms, extensive validation is required to translate this research to clinical practice. Recent optical and mechanical methods are complex and expensive and, therefore, not immediately clinically applicable. Novel osteoblast infection and tissue models best resemble infections in vivo. However, the integration of biomaterials into these models remains challenging and they require a long tissue culture, making their rapid clinical implementation unlikely. A method applicable for both clinical and research environments is difficult to realise. With a continuous increase in antimicrobial resistance, there is an urgent need for methods that analyse recurrent infections to identify the optimal treatment approaches. Graphical abstract Timeline of published and partly applied antimicrobial susceptibility testing methods, listed according to their underlying mechanism, complexity and application in research or clinics.
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Affiliation(s)
- A Schumacher
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, Room C3.577, 6229 ER, Maastricht, Netherlands.
- Science and Technology Faculty, University of Twente, Drienerlolaan 5, 7522 NB, Enschede, The Netherlands.
| | - T Vranken
- Department of Orthopaedic Surgery, CAPHRI Care and Public Health Research Institute, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - A Malhotra
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, Room C3.577, 6229 ER, Maastricht, Netherlands
| | - J J C Arts
- Department of Orthopaedic Surgery, CAPHRI Care and Public Health Research Institute, Maastricht University Medical Centre, Maastricht, The Netherlands
- Orthopaedic Biomechanics Group, Department of Biomedical Engineering, Eindhoven University of Technology (TU/e), Eindhoven, The Netherlands
| | - P Habibovic
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, Room C3.577, 6229 ER, Maastricht, Netherlands
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Chen PW, Tseng SY, Huang MS. Antibiotic Susceptibility of Commensal Bacteria from Human Milk. Curr Microbiol 2016; 72:113-119. [PMID: 26494365 DOI: 10.1007/s00284-015-0925-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 09/04/2015] [Indexed: 11/25/2022]
Abstract
Recent studies have focused on foodborne or commensal bacteria as vehicles of antibiotic resistance. However, the antibiotic resistance of milk bacteria from healthy donors is still vague in Taiwan. For this purpose, human milk samples were obtained from randomly recruited 19 healthy women between 3 and 360 days post-partum. Antibiotic susceptibility profile of bacteria from milk samples was determined. About 20 bacterial species were isolated from milk samples including Staphylococcus (6 species), Streptococcus (4 species), Enterococcus (2 species), Lactobacillus (1 species), and bacteria belonging to other genera (7 species). Some opportunistic or potentially pathogenic bacteria including Kluyvera ascorbata, Klebsiella oxytoca, Klebsiella pneumoniae, Acinetobacter baumannii, Actinomyces bovis, and Staphylococcus aureus were also isolated. Intriguingly, Staphylococcus isolates (22 strains) were resistant to 2–8 of 8 antibiotics, while Streptococcus isolates (3 strains) were resistant to 3–7 of 9 antibiotics, and members of the genus Enterococcus (5 strains) were resistant to 3–8 of 9 antibiotics. Notably, Staphylococcus lugdunensis, S. aureus, Streptococcus parasanguinis, Streptococcus pneumonia, and Enterococcus faecalis were resistant to vancomycin, which is considered as the last-resort antibiotic. Therefore, this study shows that most bacterial strains in human milk demonstrate mild to strong antibiotic resistance. Whether commensal bacteria in milk could serve as vehicles of antibiotic resistance should be further investigated.
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Affiliation(s)
- Po-Wen Chen
- Department of Nursing, St. Mary's Junior College of Medicine, Nursing and Management, Taiwan, Republic of China.
| | - Shu-Ying Tseng
- Department of Veterinary Medicine, National Chung-Hsing University, Taiwan, Republic of China
| | - Mao-Sheng Huang
- Department of Medicine Laboratory, St. Mary's Hospital Luodong, Taiwan, Republic of China
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Chang AC, Cheng CC, Wang HC, Lee WM, Shyu CL, Lin CC, Chen KS. Emphysematous pyometra secondary to Enterococcus avium infection in a dog. TIERAERZTLICHE PRAXIS AUSGABE KLEINTIERE HEIMTIERE 2016; 44:195-9. [PMID: 27111397 DOI: 10.15654/tpk-150214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 01/04/2016] [Indexed: 11/13/2022]
Abstract
A 5-year-old female intact Mastiff dog was presented with a history of vaginal discharge for 1 day. Physical examination revealed a sanguineo-purulent vaginal discharge and systemic inflammatory response syndrome. Abdominal radiographs showed several dilated and gas- filled tubular loops. The differential diagnoses included emphysematous pyometra or small intestinal mechanical ileus. Surgical exploration of the abdomen demonstrated a severely dilated and gas-filled uterus, and emphysematous pyometra was confirmed. The patient's clinical signs resolved after ovariohysterectomy. Histopathology revealed mild endometrial cystic hyperplasia with infiltration of inflammatory cells in the superficial endometrial epithelia. Enterococcus avium, an α-hemolytic gram-positive coccus, was isolated from the uterus. This paper highlights the radiographic features of emphysematous pyometra and a pathogen that has never been reported to be associated with canine pyometra previously.
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Affiliation(s)
| | | | | | | | | | | | - Kuan-Sheng Chen
- Dr. Kuan-Sheng Chen, Department of Veterinary Medicine, and Veterinary Medical Teaching Hospital, College of Veterinary Medicine, National Chung Hsing University, 250 Kuo-Kuang Road, 40227 Taichung, Taiwan,
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Rodrigues EM, Kalks KHM, Tótola MR. Prospect, isolation, and characterization of microorganisms for potential use in cases of oil bioremediation along the coast of Trindade Island, Brazil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2015; 156:15-22. [PMID: 25791233 DOI: 10.1016/j.jenvman.2015.03.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 06/04/2023]
Abstract
In the present study, acrylic coupons with a thin layer of oil on the surface were incubated in the coastal water of Trindade Island, Brazil, for 60 days. The microorganisms adhered to the coupons were isolated using enrichment medium with hexadecane and naphthalene as the sole carbon and energy source. A total of 15 bacterial isolates were obtained, and the ability of these isolates to use different hydrocarbons as the source of carbon and energy was investigated. None of the isolates produced biosurfactants under our experimental conditions. Subsequently, identification methods such as partial sequencing of the 16S rRNA gene and analysis of fatty acids (MIDI) profile were employed. Among the 15 isolates, representatives of Actinobacteria, Firmicutes, and Alphaproteobacteria were detected. The isolates Rhodococcus rhodochrous TRN7 and Nocardia farcinica TRH1 were able to use all the hydrocarbons added to the culture medium (toluene, octane, xylene, naphthalene, phenanthrene, pyrene, hexadecane, anthracene, eicosane, tetracosane, triacontane, and pentacontane). Polymerase chain reaction amplification of the DNA isolated by employing primers for catechol 2,3-dioxygenase, alkane dehydrogenase and the alpha subunit of hydroxylating dioxygenases polycyclic aromatic hydrocarbon rings genes demonstrated that various isolates capable of utilizing hydrocarbons do not exhibit genes of known routes of catabolism, suggesting the existence of unknown catabolic pathways in these microorganisms. Our findings suggest that the microbiota associated to the coast of tropical oceanic islands has the ability to assist in environmental regeneration in cases of accidents involving oil spills in its shore. Thus, it motivates studies to map bioremediation strategies using the autochthonous microbiota from these environments.
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Affiliation(s)
- Edmo M Rodrigues
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| | - Karlos H M Kalks
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Marcos R Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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Review of Salmonella detection and identification methods: Aspects of rapid emergency response and food safety. Food Control 2015. [DOI: 10.1016/j.foodcont.2014.07.011] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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12
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Hałasa R, Turecka K, Orlewska C, Werel W. Comparison of fluorescence optical respirometry and microbroth dilution methods for testing antimicrobial compounds. J Microbiol Methods 2014; 107:98-105. [PMID: 25307692 DOI: 10.1016/j.mimet.2014.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/26/2014] [Accepted: 09/27/2014] [Indexed: 10/24/2022]
Abstract
An analysis of the usefulness of the fluorescence optical respirometry test method to study several antimicrobials was performed. An oxygen-sensitive sensor: ruthenium-tris(4,7-diphenyl-1,10-phenanthroline) dichloride (Ru(DPP)3Cl2), the phosphorescence of which is quenched by molecular oxygen, was synthesised according to a method modified by us and then applied. A prototype sensitive measurement system was designed and constructed. Analyses of the impact of various antimicrobial chemical factors were performed: ampicillin, co-trimoxazole, nystatin, and newly synthesised compounds. It was shown that optical respirometry allows for analysis of the culture growth kinetics of bacteria and fungi and determination of cell growth parameters. It was shown also that MIC values obtained by fluorescence optical respirometry are consistent with the results of the MIC determinations made by serial dilution method (traditional MIC testing using CLSI). The method allows the time to obtain results to be significantly reduced (from 24-48 h to 5-7 h for bacteria and 24 yeasts) and allows the effect of concentrations below the MIC for the metabolic activity of microorganisms to be monitored. The sensitivity of the method allowed the volume of the tested samples to be lessened from 160 μl to 50 μl. Fluorescence optical respirometry allows for the rapid detection and evaluation of the action of various chemical compounds on the metabolic activity of microorganisms in real-time measurement of fluorescence intensity.
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Affiliation(s)
- R Hałasa
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, al. Hallera 107, 80-416 Gdańsk, Poland.
| | - K Turecka
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, al. Hallera 107, 80-416 Gdańsk, Poland
| | - C Orlewska
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, al. Hallera 107, 80-416 Gdańsk, Poland
| | - W Werel
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, al. Hallera 107, 80-416 Gdańsk, Poland
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Benga L, Benten WPM, Engelhardt E, Köhrer K, Gougoula C, Sager M. 16S ribosomal DNA sequence-based identification of bacteria in laboratory rodents: a practical approach in laboratory animal bacteriology diagnostics. Lab Anim 2014; 48:305-12. [PMID: 24876090 DOI: 10.1177/0023677214538240] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Correct identification of bacteria is crucial for the management of rodent colonies. Some bacteria are difficult to identify phenotypically outside reference laboratories. In this study, we evaluated the utility of 16S ribosomal DNA (rDNA) sequencing as a means of identifying a collection of 30 isolates of rodent origin which are conventionally difficult to identify. Sequence analysis of the first approximate 720 to 880 bp of the 5'- end of 16S rDNA identified 25 isolates (83.33%) with ≥ 99% similarity to a sequence of a type strain, whereas three isolates (10%) displayed a sequence similarity ≥ 97% but <99% to the type strain sequences. These similarity scores were used to define identification to species and genus levels, respectively. Two of the 30 isolates (6.67%) displayed a sequence similarity of ≥ 95 but <97% to the reference strains and were thus allocated to a family. This technique allowed us to document the association of mice with bacteria relevant for the colonies management such as Pasteurellaceae, Bordetella hinzii or Streptococcus danieliae. In addition, human potential pathogens such as Acinetobacter spp., Ochrobactrum anthropi and Paracoccus yeei or others not yet reported in mouse bacterial species such as Leucobacter chironomi, Neisseria perflava and Pantoea dispersa were observed. In conclusion, the sequence analysis of 16S rDNA proved to be a useful diagnostic tool, with higher performance characteristics than the classical phenotypic methods, for identification of laboratory animal bacteria. For the first time this method allowed us to document the association of certain bacterial species with the laboratory mouse.
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Affiliation(s)
- Laurentiu Benga
- Animal Research Facility, Heinrich Heine University Düsseldorf, University Hospital, Düsseldorf, Germany
| | - W Peter M Benten
- Animal Research Facility, Heinrich Heine University Düsseldorf, University Hospital, Düsseldorf, Germany
| | - Eva Engelhardt
- Animal Research Facility, Heinrich Heine University Düsseldorf, University Hospital, Düsseldorf, Germany
| | - Karl Köhrer
- Biological and Medical Research Center (BMFZ), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christina Gougoula
- Animal Research Facility, Heinrich Heine University Düsseldorf, University Hospital, Düsseldorf, Germany
| | - Martin Sager
- Animal Research Facility, Heinrich Heine University Düsseldorf, University Hospital, Düsseldorf, Germany
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Park SH, Aydin M, Khatiwara A, Dolan MC, Gilmore DF, Bouldin JL, Ahn S, Ricke SC. Current and emerging technologies for rapid detection and characterization of Salmonella in poultry and poultry products. Food Microbiol 2014; 38:250-62. [DOI: 10.1016/j.fm.2013.10.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 07/28/2013] [Accepted: 10/04/2013] [Indexed: 12/19/2022]
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15
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Blackett KL, Siddhi SS, Cleary S, Steed H, Miller MH, Macfarlane S, Macfarlane GT, Dillon JF. Oesophageal bacterial biofilm changes in gastro-oesophageal reflux disease, Barrett's and oesophageal carcinoma: association or causality? Aliment Pharmacol Ther 2013; 37:1084-92. [PMID: 23600758 DOI: 10.1111/apt.12317] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 09/01/2012] [Accepted: 03/30/2013] [Indexed: 12/17/2022]
Abstract
SUMMARY Barrett's oesophagus (BO) and gastro-oesophageal reflux disease (GERD) are precursors of oesophageal adenocarcinoma (OAC). There is an oesophageal biofilm, which changes in disease, but its role in aetiopathogenesis remains unclear. AIM To define the oesophageal microbiota of patients with GERD, BO and OAC compared with controls and to investigate mucosal responses related to the microbiota. METHODS Cultural analysis identified the dominant bacterial species from a subset of each disease group. Based on this, molecular techniques were used to define the cohort. Host responses were analysed in tissues and co-culture experiments. RESULTS A total of 111 species belonging to 26 genera were isolated. There was a significant decrease in bacterial counts in the GERD and BO groups for all genera except Campylobacter, which colonised GERD and Barrett's patients in increasing numbers. Campylobacter concisus was the dominant species. This relationship was not seen in the cancer group. Significant increases in IL-18 were seen in GERD and BO colonised by Campylobacter. CONCLUSIONS This study defines differences in the oesophageal biofilm in disease states, revealing the emergence of C. concisus as the dominant new colonist in the refluxed oesophagus. We also associate the presence of these bacteria with increased expression of cytokines related to carcinogenesis.
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Affiliation(s)
- K L Blackett
- Gut Group, Biomedical Research Institute, University of Dundee, Dundee, UK
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16
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Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli. Proc Natl Acad Sci U S A 2012; 109:E2561-8. [PMID: 22908292 DOI: 10.1073/pnas.1209742109] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Cell size varies greatly among different types of cells, but the range in size that a specific cell type can reach is limited. A long-standing question in biology is how cells control their size. Escherichia coli adjusts size and growth rate according to the availability of nutrients so that it grows larger and faster in nutrient-rich media than in nutrient-poor media. Here, we describe how, using classical genetics, we have isolated a remarkably small E. coli mutant that has undergone a 70% reduction in cell volume with respect to wild type. This mutant lacks FabH, an enzyme involved in fatty acid biosynthesis that previously was thought to be essential for the viability of E. coli. We demonstrate that although FabH is not essential in wild-type E. coli, it is essential in cells that are defective in the production of the small-molecule and global regulator ppGpp. Furthermore, we have found that the loss of FabH causes a reduction in the rate of envelope growth and renders cells unable to regulate cell size properly in response to nutrient excess. Therefore we propose a model in which fatty acid biosynthesis plays a central role in regulating the size of E. coli cells in response to nutrient availability.
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17
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Motoshima M, Yanagihara K, Morinaga Y, Matsuda J, Hasegawa H, Kohno S, Kamihira S. Identification of bacteria directly from positive blood culture samples by DNA pyrosequencing of the 16S rRNA gene. J Med Microbiol 2012; 61:1556-1562. [PMID: 22899780 DOI: 10.1099/jmm.0.049163-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rapid identification of the causative bacteria of sepsis in patients can contribute to the selection of appropriate antibiotics and improvement of patients' prognosis. Genotypic identification is an emerging technology that may provide an alternative method to, or complement, established phenotypic identification procedures. We evaluated a rapid protocol for bacterial identification based on PCR and pyrosequencing of the V1 and V3 regions of the 16S rRNA gene using DNA extracted directly from positive blood culture samples. One hundred and two positive blood culture bottles from 68 patients were randomly selected and the bacteria were identified by phenotyping and pyrosequencing. The results of pyrosequencing identification displayed 84.3 and 64.7 % concordance with the results of phenotypic identification at the genus and species levels, respectively. In the monomicrobial samples, the concordance between the results of pyrosequencing and phenotypic identification at the genus level was 87.0 %. Pyrosequencing identified one isolate in 60 % of polymicrobial samples, which were confirmed by culture analysis. Of the samples identified by pyrosequencing, 55.7 % showed consistent results in V1 and V3 targeted sequencing; other samples were identified based on the results of V1 (12.5 %) or V3 (31.8 %) sequencing alone. One isolate was erroneously identified by pyrosequencing due to high sequence similarity with another isolate. Pyrosequencing identified one isolate that was not detected by phenotypic identification. The process of pyrosequencing identification can be completed within ~4 h. The information provided by DNA-pyrosequencing for the identification of micro-organisms in positive blood culture bottles is accurate and could prove to be a rapid and useful tool in standard laboratory practice.
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Affiliation(s)
- Maiko Motoshima
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yoshitomo Morinaga
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Junichi Matsuda
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroo Hasegawa
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shigeru Kohno
- Global COE Program, Nagasaki University, Nagasaki, Japan.,Second Department of Internal Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shimeru Kamihira
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Kootallur BN, Thangavelu CP, Mani M. Bacterial identification in the diagnostic laboratory: how much is enough? Indian J Med Microbiol 2012; 29:336-40. [PMID: 22120791 DOI: 10.4103/0255-0857.90156] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The major impetus for bacterial identification came after the advent of solid culture media. Morphological appearance of bacterial colonies was often sufficient for their identification in the laboratory. Even in modern times, preliminary identification of most cultivable bacteria is based on such morphological characters. Advances have been made media for the presumptive identification of common organisms encountered in clinical samples. Phenotypic characterisation of bacteria with, physiological tests with a battery of biochemical tests differentiate related bacterial genera as well as confirm their identity. . Each laboratory can select its own method(s) of identification, provided they are based on scientific / epidemiological evidence; clinical laboratory and standards institute (CLSI) is a widely accepted organization and laboratories in many parts of the world follow its recommendations for bacterial identification. Some of the latest advances in identification include Matrix Assisted Laser Desorption Ionization - Time of Flight Mass Spectroscopy (MALDI-TOF) is a state of art facility used for fast and reliable species-specific identification of bacteria including Mycobacteria and fungi including yeasts. However the single most important factor that decides the method of bacterial identification in any laboratory is the cost involved. In the final analysis, selection of tests for bacterial identification should be based on their standardization with proper scientific basis. Considering the cost and lack of easy availability of commercial kits, we have put forward a simplified and rapid method of identification for most commonly encountered bacterial pathogens causing human infection in India.
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Affiliation(s)
- B N Kootallur
- Microbiological Laboratory, 12A Cowley Brown Road (East), RS Puram, Coimbatore - 641 002, India.
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López-Campos G, Martínez-Suárez JV, Aguado-Urda M, López-Alonso V. Detection, Identification, and Analysis of Foodborne Pathogens. SPRINGERBRIEFS IN FOOD, HEALTH, AND NUTRITION 2012. [DOI: 10.1007/978-1-4614-3250-0_2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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20
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Endimiani A, Hujer KM, Hujer AM, Kurz S, Jacobs MR, Perlin DS, Bonomo RA. Are we ready for novel detection methods to treat respiratory pathogens in hospital-acquired pneumonia? Clin Infect Dis 2011; 52 Suppl 4:S373-83. [PMID: 21460299 PMCID: PMC3106236 DOI: 10.1093/cid/cir054] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hospital-acquired pneumonia represents one of the most difficult treatment challenges in infectious diseases. Many studies suggest that the timely administration of appropriate, pathogen-directed therapy can be lifesaving. Because results of culture and antimicrobial susceptibility testing can take 48 h or longer, physicians currently rely on clinical, epidemiological, and demographic factors to assist with the choice of empiric therapy for antibiotic-resistant pathogens. At present, a number of rapid molecular tests are being developed that identify pathogens and the presence of genetic determinants of antimicrobial resistance (eg, GeneXpert [Cepheid], ResPlex [Qiagen], FilmArray [Idaho Technologies], and Microarray [Check-Points]). In this review, the potential impact that molecular diagnostics has to identify and characterize pathogens that cause hospital-acquired bacterial pneumonia at an early stage is examined. In addition, a perspective on a novel technology, polymerase chain reaction followed by electrospray ionization mass spectrometry, is presented, and its prospective use in the diagnosis of pneumonia is also discussed. The complexities of the pulmonary microbiome represent a novel challenge to clinicians, but many questions still remain even as these technologies improve.
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Affiliation(s)
- Andrea Endimiani
- Department of Medicine
- Department of Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Kristine M. Hujer
- Department of Medicine
- Department of Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Andrea M. Hujer
- Department of Medicine
- Department of Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Sebastian Kurz
- Department of Medicine
- Department of Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | | | - David S. Perlin
- Public Health Research Institute
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Robert A. Bonomo
- Department of Medicine
- Department of Pharmacology
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine
- Department of Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
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Halket G, Dinsdale A, Logan N. Evaluation of the VITEK2 BCL card for identification of Bacillus species and other aerobic endosporeformers. Lett Appl Microbiol 2010; 50:120-6. [DOI: 10.1111/j.1472-765x.2009.02765.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Comparison of the Biolog OmniLog Identification System and 16S ribosomal RNA gene sequencing for accuracy in identification of atypical bacteria of clinical origin. J Microbiol Methods 2009; 79:336-43. [DOI: 10.1016/j.mimet.2009.10.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2008] [Revised: 10/06/2009] [Accepted: 10/07/2009] [Indexed: 02/01/2023]
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23
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Torres E, Villanueva R, Bou G. Comparison of different methods of determining β-lactam susceptibility in clinical strains of Pseudomonas aeruginosa. J Med Microbiol 2009; 58:625-629. [DOI: 10.1099/jmm.0.005587-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
One hundred and one randomly selected (2003–2005) clinical isolates ofPseudomonas aeruginosawere used to assess the quantitative (MIC) and qualitative (susceptibility category) agreement between the microdilution broth reference method (RM) and disc diffusion (DD), Etest and the VITEK 2 automated susceptibility test system for determination of the susceptibility ofP. aeruginosato piperacillin (PIP), PIP–tazobactam (TZP), ceftazidime (CAZ), aztreonam (ATM) cefepime (FEP) and imipenem (IMP). The results obtained by the RM were compared with those obtained by the other methods. The RM and DD were performed according to CLSI criteria. Etest and VITEK 2 were according to the manufacturer's instructions. The Advanced Expert System (AES), which interprets MICs generated by VITEK 2, was modified with new rules of interpretation. Overall, VITEK 2 showed the lowest MIC90values for the six antibiotics. The RM categorical testing (susceptibility and resistance) rates withP. aeruginosawere 11.8 and 88.1 for PIP, 22.7 and 77.2 for TZP, 14.8 and 78.2 for CAZ, 12.8 and 54.4 for ATM, 16.8 and 75.3 for FEP, and 7.9 and 90.1 for IMP, respectively. Very major errors (false susceptible) were only detected for ATM and FEP with DD and for IMP with three methods. Major errors (false resistant) were generally acceptable for all antibiotics except TZP. VITEK 2 yielded a high level of minor errors (trends toward false susceptibility), mainly with CAZ and FEP. A good agreement was obtained for all antibiotics/methods assayed, thus highlighting the importance of the AES for categorization ofβ-lactam susceptibility inP. aeruginosa.
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Affiliation(s)
- Eva Torres
- Servicio de Microbiología – Unidad de Investigación, Complejo Hospitalario Universitario Juan Canalejo, La Coruña, Spain
| | - Rosa Villanueva
- Servicio de Microbiología – Unidad de Investigación, Complejo Hospitalario Universitario Juan Canalejo, La Coruña, Spain
| | - Germán Bou
- Servicio de Microbiología – Unidad de Investigación, Complejo Hospitalario Universitario Juan Canalejo, La Coruña, Spain
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Gilad J, Giladi M, Schwartz D. Candida albicans masquerading as gram-negative bacilli in the clinical laboratory. ACTA ACUST UNITED AC 2007; 39:907-10. [PMID: 17852917 DOI: 10.1080/00365540701402996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We report misidentification of Candida albicans as Gram-negative bacilli owing to colony morphology on MacConkey agar and subsequent inoculation into GN-ID/VITEK-2. ATCC and clinical Candida strains (n = 24) masqueraded as various bacterial species when experimentally inoculated into GN-ID cards. This phenomenon should be considered when peculiar taxa or susceptibility are encountered.
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Affiliation(s)
- Jacob Gilad
- Clinical Microbiology Laboratory, Tel-Aviv Sourasky Medical Centre, Tel-Aviv, Israel.
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25
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Valenza G, Ruoff C, Vogel U, Frosch M, Abele-Horn M. Microbiological evaluation of the new VITEK 2 Neisseria-Haemophilus identification card. J Clin Microbiol 2007; 45:3493-7. [PMID: 17728469 PMCID: PMC2168501 DOI: 10.1128/jcm.00953-07] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
VITEK 2 is an automated identification system for diverse bacterial and fungal species. A new card (the Neisseria-Haemophilus [NH] card) for the identification of Neisseria spp., Haemophilus spp., and other fastidious gram-negative or gram-variable microorganisms has been developed, but its performance in a routine clinical laboratory has not yet been evaluated. In this study, a total of 188 bacterial strains belonging to the genera Actinobacillus, Campylobacter, Capnocytophaga, Cardiobacterium, Eikenella, Gardnerella, Haemophilus, Kingella, Moraxella, and Neisseria were investigated. The NH card was able to identify 171 strains (91%) correctly without the need for extra tests; one strain (0.5%) was misidentified, and five strains (2.7%) could not be classified. Eleven strains (5.8%) were identified with a low level of discrimination, and simple additional tests were required to increase the correct-identification rate to 96.8%. The results were available within 6 h. Based on these results, the new VITEK 2 NH card appears to be a good method for the identification of diverse groups of fastidious organisms, which would otherwise require testing with multiple systems. However, more work is needed to evaluate the performance of VITEK 2 with regard to Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella bacteria because of the insufficient number of strains tested in this study. Moreover, further reduction of the detection time would be desirable.
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Affiliation(s)
- Giuseppe Valenza
- Institute of Hygiene and Microbiology, University of Würzburg, Josef-Schneider-Str 2/E1, 97080, Würzburg, Germany.
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Luna RA, Fasciano LR, Jones SC, Boyanton BL, Ton TT, Versalovic J. DNA pyrosequencing-based bacterial pathogen identification in a pediatric hospital setting. J Clin Microbiol 2007; 45:2985-92. [PMID: 17652476 PMCID: PMC2045277 DOI: 10.1128/jcm.00630-07] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sole reliance on biochemical methods can limit the clinical microbiology laboratory's ability to identify bacterial pathogens. This study describes the incorporation of DNA pyrosequencing-based identification for routine pathogen identification of atypical clinical isolates in a large children's hospital. The assay capitalized on the highly conserved nature of 16S rRNA genes by positioning amplification and sequencing primers in conserved target sequences flanking the variable V1 and V3 regions. A total of 414 isolates of 312 pediatric patients were tested by DNA pyrosequencing during the time period from December 2003 to July 2006. Seventy-eight different genera were specified by DNA pyrosequencing, and isolates were derived from diverse specimen types. By integrating DNA sequencing of bacterial pathogens with conventional microbiologic methods, isolates that lacked a definitive identification by biochemical testing yielded genus- or species-level identifications in approximately 90% of cases by pyrosequencing. Improvements incorporated into the assay process during the period of clinical testing included software enhancements, improvements in sequencing reagents, and refinements in database search strategies. Coupled with isolation by bacteriologic culture and biochemical testing, DNA pyrosequencing-based bacterial identification was a valuable tool that markedly improved bacterial pathogen identification in a pediatric hospital setting.
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Affiliation(s)
- Ruth Ann Luna
- Division of Molecular Pathology, Department of Pathology, Texas Children's Hospital, Houston, Texas 77030, USA
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27
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Kulwichit W, Nilgate S, Chatsuwan T, Krajiw S, Unhasuta C, Chongthaleong A. Accuracies of Leuconostoc phenotypic identification: a comparison of API systems and conventional phenotypic assays. BMC Infect Dis 2007; 7:69. [PMID: 17605772 PMCID: PMC1947989 DOI: 10.1186/1471-2334-7-69] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2006] [Accepted: 07/02/2007] [Indexed: 11/10/2022] Open
Abstract
Background Commercial diagnostics are commonly used to identify gram-positive bacteria. Errors have been reported mostly at the species level. We have found certain phenotypic criteria used in API systems which significantly misidentify Leuconostoc, an emerging human pathogen, at the genus level. We also attempt to find practical, conventional phenotypic assays for accurate identification of this group of bacteria. Methods Clinical isolates of catalase-negative, gram-positive coccoid or coccobacillary bacteria with non-β hemolysis in our institute during 1997–2004 were subject to an identification aid by API 20 STREP, following the instruction manual, as an aid to conventional phenotypic tests. Those identified as Leuconostoc by API 20 STREP were re-examined by the same kit and also by API 50 CHL according to the instruction manuals, by our Leuconostoc conventional phenotypic assays, by Leuconostoc- and Lactobacillus-specific PCR's, and, where possible, by 16S rDNA sequence analysis. In addition, catalase-negative gram-positive isolates during 2005–2006 which were resistant to vancomycin at high levels were also evaluated by the same phenotypic and genotypic assays. Results Out of several thousands of clinical gram-positive isolates, 26 catalase negative gram-positive isolates initially identified as Leuconostoc by API 20 STREP and 7 vancomycin-resistant gram-positive catalase-negative bacteria entered the study. 11 out of the 26 isolates and all the 7 isolates were identified as Leuconostoc by API 20 STREP. Only 5 isolates, however, were confirmed by both genotypic and all defined conventional phenotypic criteria. API 50 CHL also failed to reliably provide accurate identification of Leuconostoc. We have identified key problem tests in API 20 STREP leading to misidentification of the bacteria. A simple, conventional set of phenotypic tests for Leuconostoc identification is proposed. Conclusion The current API systems cannot accurately identify Leuconostoc. Identification of vancomycin-resistant, catalase-negative gram-positive bacteria should be performed by a few practical phenotypic assays, with assistance of genotypic assays where available.
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Affiliation(s)
- Wanla Kulwichit
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sumanee Nilgate
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sunisa Krajiw
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chudaachhara Unhasuta
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Anan Chongthaleong
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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KALAMAKI MARY, PRICE ROBERTJ, FUNG DANIELY. RAPID METHODS FOR IDENTIFYING SEAFOOD MICROBIAL PATHOGENS AND TOXINS1. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1745-4581.1997.tb00155.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Tokajian S, Hashwa F. Incidence of antibiotic resistance in coliforms from drinking water and their identification using the Biolog and the API identification systems. J Chemother 2004; 16:45-50. [PMID: 15077998 DOI: 10.1179/joc.2004.16.1.45] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Antibiotic-resistant bacteria were common in samples collected from an intermittent water distribution system in Lebanon. Multiply-resistant isolates were also present and most commonly to amoxycillin, cephalexin and sulfamethoxazole/trimethoprim. The aminoglycosides (amikacin, gentamicin and kanamycin) were the most effective, with almost all tested strains showing susceptibility to these antimicrobial agents. Both the Biolog GN MicroPlates and the API 20E strips can be used for the identification of coliform bacteria isolated from potable water, but the outcome of the identification should be viewed with caution. 51% of isolates were assigned similar identities by both the Biolog MicroPlates and the API 20E strips. The similarity at the species level was lower (33%) compared to that at the genus level (67%). The identification of Escherichia coli strains, which represented 30% of all tested organisms, showed 95% similarity in the assigned genus and species using both identification schemes.
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Affiliation(s)
- S Tokajian
- The Lebanese American University, Byblos, Lebanon
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García-López I, Otero A, García-López ML, Santos JA. Molecular and phenotypic characterization of nonmotile Gram-negative bacteria associated with spoilage of freshwater fish. J Appl Microbiol 2004; 96:878-86. [PMID: 15012828 DOI: 10.1111/j.1365-2672.2004.02214.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS Characterization of nonmotile bacteria associated with freshwater fish spoilage and that phenotypically resembled Psychrobacter spp. METHODS AND RESULTS A population of 44 nonmotile Gram-negative rods could not be assigned to the genus Psychrobacter on the basis of a definitive test (transformation assay). Conventional and commercial phenotypic systems did not help in identification. A second extensive phenotypic analysis using different temperatures and media confirmed these isolates as nonmotile although electron microscopic examination showed that all but two had one to four polar flagella and other appendages. On the basis of numerical taxonomy, this population was divided into six clusters, one of them consisting of five fluorescent strains. Sequencing of fluorescent and non fluorescent representative strains from each cluster demonstrated that strains from five clusters had between 97.8 and 98.8% sequence homology with Pseudomonas fragi IFO 3458. This and an unknown strain from deep sea were the closest organisms (80.9% sequence homology) to one aflagellated representative strain of the remaining cluster. CONCLUSIONS Oxidase-positive, nonmotile, nonfermenter Gram-negative rods isolated from freshwater fish can be wrongly ascribed to the genus Psychrobacter. SIGNIFICANCE AND IMPACT OF THE STUDY Molecular methods are necessary for the identification of environmental isolates and species with an incomplete phenotypic description. This work emphasizes the need for a sound description of Ps. fragi based on molecular and phenotypic characterization.
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Affiliation(s)
- I García-López
- Department of Food Hygiene and Food Technology, Veterinary Faculty, University of León, León, Spain
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Donay JL, Mathieu D, Fernandes P, Prégermain C, Bruel P, Wargnier A, Casin I, Weill FX, Lagrange PH, Herrmann JL. Evaluation of the automated phoenix system for potential routine use in the clinical microbiology laboratory. J Clin Microbiol 2004; 42:1542-6. [PMID: 15071001 PMCID: PMC387561 DOI: 10.1128/jcm.42.4.1542-1546.2004] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Revised: 09/01/2003] [Accepted: 01/07/2004] [Indexed: 11/20/2022] Open
Abstract
A comparative study was designed to evaluate the identification (ID) and antimicrobial susceptibility testing (AST) performances of the BD Phoenix Automated Microbiology System (Becton Dickinson Diagnostic Systems [BD], Pont de Claix, France). A total of 305 single clinical isolates were collected, and comparisons were made with routine manual methods in use in our microbiology laboratories. The percentages of correct IDs were 93.3, 89.4, 91.8, and 85.7% for enterobacteria, nonfermenting gram-negative bacilli, staphylococci, and streptococci-enterococci, respectively. The median ID time was 3 h, and the median time for AST was 10 h 30 min. AST results showed variable percentages of errors for the different antibiotics. None of the enterobacteria and 0.3% of Pseudomonas aeruginosa isolates showed a very major error (VME). Only one strain of Staphylococcus aureus showed a VME with oxacillin. We demonstrate here the efficiency of the Phoenix system, which can be used for the majority of strains encountered in a university-based laboratory, for ID and AST.
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Affiliation(s)
- J-L Donay
- Service de Microbiologie, Hôpital Saint Louis, Paris, France
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Bruins MJ, Bloembergen P, Ruijs GJHM, Wolfhagen MJHM. Identification and susceptibility testing of Enterobacteriaceae and Pseudomonas aeruginosa by direct inoculation from positive BACTEC blood culture bottles into Vitek 2. J Clin Microbiol 2004; 42:7-11. [PMID: 14715724 PMCID: PMC321735 DOI: 10.1128/jcm.42.1.7-11.2004] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Inoculation of an automated system for rapid identification (ID) and antimicrobial susceptibility testing (AST) directly from positive blood culture bottles will reduce the turnaround time of laboratory diagnosis of septicemic patients, which benefits clinical outcome and decreases patient costs. Direct test results, however, must always be confirmed by testing a pure overnight culture, which is the "gold standard." We studied the accuracy of direct testing versus repeat testing in order to investigate the possibility of refraining from repeat testing. We also assessed the clinical risk of reporting results based on direct testing only. We inoculated Vitek 2 (bioMérieux) directly from 410 positive BACTEC 9240 (BD) blood culture bottles containing gram-negative rods and studied the ID and AST results. In a comparison of direct inoculation with the standard method, a total of 344 isolates of Enterobacteriaceae and Pseudomonas aeruginosa were tested, and 93.0% were correctly identified. Of the 39 (10.2%) samples that contained bacilli not identifiable by Vitek 2, only 1 gave a conclusive, correct result. The overall MIC agreement among 312 isolates was 99.2%, with 0.8% very major and 0.02% major error rates. Of only three (polymicrobial) samples, the direct susceptibility pattern would be reported to the clinician as too sensitive. Vitek 2 results obtained from direct inoculation of blood culture bottles containing gram-negative bacilli are safe enough for immediate reporting, provided that ID and AST are consistent. Repeat testing is not necessary, unless Gram stain or overnight subculture results raise doubt about the purity of the culture.
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Affiliation(s)
- Marjan J Bruins
- Laboratory of Clinical Microbiology and Infectious Diseases, Isala Klinieken, 8021 AM Zwolle, The Netherlands.
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Rodrigues M, Ho P, López-Caballero M, Vaz-Pires P, Nunes M. Characterization and identification of microflora from soaked cod and respective salted raw materials. Food Microbiol 2003. [DOI: 10.1016/s0740-0020(02)00086-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Himmelreich U, Somorjai RL, Dolenko B, Lee OC, Daniel HM, Murray R, Mountford CE, Sorrell TC. Rapid identification of Candida species by using nuclear magnetic resonance spectroscopy and a statistical classification strategy. Appl Environ Microbiol 2003; 69:4566-74. [PMID: 12902244 PMCID: PMC169103 DOI: 10.1128/aem.69.8.4566-4574.2003] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectra were acquired from suspensions of clinically important yeast species of the genus Candida to characterize the relationship between metabolite profiles and species identification. Major metabolites were identified by using two-dimensional correlation NMR spectroscopy. One-dimensional proton NMR spectra were analyzed by using a staged statistical classification strategy. Analysis of NMR spectra from 442 isolates of Candida albicans, C. glabrata, C. krusei, C. parapsilosis, and C. tropicalis resulted in rapid, accurate identification when compared with conventional and DNA-based identification. Spectral regions used for the classification of the five yeast species revealed species-specific differences in relative amounts of lipids, trehalose, polyols, and other metabolites. Isolates of C. parapsilosis and C. glabrata with unusual PCR fingerprinting patterns also generated atypical NMR spectra, suggesting the possibility of intraspecies discontinuity. We conclude that NMR spectroscopy combined with a statistical classification strategy is a rapid, nondestructive, and potentially valuable method for identification and chemotaxonomic characterization that may be broadly applicable to fungi and other microorganisms.
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Affiliation(s)
- Uwe Himmelreich
- Centre for Infectious Diseases and Microbiology, Institute for Clinical Pathology and Medical Research, University of Sydney at Westmead Hospital, Westmead, New South Wales 2145, Australia.
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35
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Choi SS, Lee JW, Kang BY, Ha NJ. Antimicrobial resistance patterns of vancomycin-resistant Streptococcus equinus isolated from animal foods and epidemiological typing of resistant S. equinus by microbial uniprimer kit. Arch Pharm Res 2003; 26:638-43. [PMID: 12967199 DOI: 10.1007/bf02976713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Raw milk samples, and cow and chicken intestines were tested to isolate vancomycin-resistant, gram-positive bacteria. From these samples, we isolated seven vancomycin-resistant Streptococcus equinus, two vancomycin-resistant viridans Streptococcus and two vancomycin-resistant Enterococcus faecium. The MICs of several antibiotics, including vancomycin, against these strains were tested. Seven isolates of S. equinus showed high level resistance to vancomycin and teicoplanin (>100 microg/mL). The cell wall thickness of these strains was compared with that of the sensitive strain by TEM and no differences were obserbed between these strains. We compared the strains of vancomycin-resistant Streptococcus equinus using PCR with Microbial Uniprimer Kit. We concluded that it is necessary to combine other methods in order to cluster and identify all isolates of S. equinus.
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Affiliation(s)
- Sung-Sook Choi
- Department of Food Science, Sahmyook College, Seoul 139-742, Korea
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36
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Gavin PJ, Warren JR, Obias AA, Collins SM, Peterson LR. Evaluation of the Vitek 2 system for rapid identification of clinical isolates of gram-negative bacilli and members of the family Streptococcaceae. Eur J Clin Microbiol Infect Dis 2002; 21:869-74. [PMID: 12525922 DOI: 10.1007/s10096-002-0826-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accuracy of the Vitek 2 automated system (bioMérieux Vitek, USA) for rapid identification of bacteria was evaluated using a collection of 858 epidemiologically unrelated gram-negative and 99 gram-positive clinical isolates. Isolates were tested after subculturing to ensure purity. Conventional agar-based biochemical tests (Steers replicator) were used as a reference method of identification. Gram-negative bacteria were identified to the species level with 95.3% accuracy by the system ( Enterobacteriaceae, 95.9%; and non- Enterobacteriaceae, 92.5%), and gram-positive isolates with 72% accuracy. Although Vitek 2 identified routine clinical isolates of gram-negative bacilli and Enterococcus faecalis and Enterococcus faecium reliably, rapidly, and reproducibly, improvement is required in the identification of less common species of enterococci and viridans group streptococci.
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Affiliation(s)
- P J Gavin
- Department of Pathology, Northwestern Memorial Hospital and Northwestern University Medical School, Chicago, IL 60201, USA
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Maquelin K, Kirschner C, Choo-Smith LP, van den Braak N, Endtz HP, Naumann D, Puppels GJ. Identification of medically relevant microorganisms by vibrational spectroscopy. J Microbiol Methods 2002; 51:255-71. [PMID: 12223286 DOI: 10.1016/s0167-7012(02)00127-6] [Citation(s) in RCA: 509] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the recent years, vibrational spectroscopies (infrared and Raman spectroscopy) have been developed for all sorts of analyses in microbiology. Important features of these methods are the relative ease with which measurements can be performed. Furthermore, in order to obtain infrared or Raman spectra, there is only a limited amount of sample handling involved without the need for expensive chemicals, labels or dyes. Here, we review the potential application of vibrational spectroscopies for the use in medical microbiology. After describing some of the basics of the techniques, considerations on reproducibility and standardisation are presented. Finally, the use of infrared and Raman spectroscopy for the (rapid) identification of medically relevant microorganisms is discussed. It can be concluded that vibrational spectroscopies show high potential as novel methods in medical microbiology.
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Affiliation(s)
- K Maquelin
- Laboratory for Intensive Care Research and Optical Spectroscopy, Department of General Surgery 10M, Erasmus MC, University Medical Center Rotterdam, Dr Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
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Affiliation(s)
- J Michael Janda
- Microbial Diseases Laboratory, Division of Communicable Disease Control, California Department of Health Services, Berkeley, California 94704-1011, USA.
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39
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Ligozzi M, Bernini C, Bonora MG, De Fatima M, Zuliani J, Fontana R. Evaluation of the VITEK 2 system for identification and antimicrobial susceptibility testing of medically relevant gram-positive cocci. J Clin Microbiol 2002; 40:1681-6. [PMID: 11980942 PMCID: PMC130656 DOI: 10.1128/jcm.40.5.1681-1686.2002] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2001] [Revised: 09/27/2001] [Accepted: 02/05/2002] [Indexed: 11/20/2022] Open
Abstract
A study was conducted to evaluate the new VITEK 2 system (bioMérieux) for identification and antibiotic susceptibility testing of gram-positive cocci. Clinical isolates of Staphylococcus aureus (n = 100), coagulase-negative staphylococci (CNS) (n = 100), Enterococcus spp. (n = 89), Streptococcus agalactiae (n = 29), and Streptococcus pneumoniae (n = 66) were examined with the ID-GPC identification card and with the AST-P515 (for staphylococci), AST-P516 (for enterococci and S. agalactiae) and AST-P506 (for pneumococci) susceptibility cards. The identification comparison methods were the API Staph for staphylococci and the API 20 Strep for streptococci and enterococci; for antimicrobial susceptibility testing, the agar dilution method according to the procedure of the National Committee for Clinical Laboratory Standards (NCCLS) was used. The VITEK 2 system correctly identified to the species level (only one choice or after simple supplementary tests) 99% of S. aureus, 96.5% of S. agalactiae, 96.9% of S. pneumoniae, 92.7% of Enterococcus faecalis, 91.3% of Staphylococcus haemolyticus, and 88% of Staphylococcus epidermidis but was least able to identify Enterococcus faecium (71.4% correct). More than 90% of gram-positive cocci were identified within 3 h. According to the NCCLS breakpoints, antimicrobial susceptibility testing with the VITEK 2 system gave 96% correct category agreement, 0.82% very major errors, 0.17% major errors, and 2.7% minor errors. Antimicrobial susceptibility testing showed category agreement from 94 to 100% for S. aureus, from 90 to 100% for CNS, from 91 to 100% for enterococci, from 96 to 100% for S. agalactiae, and from 91 to 100% for S. pneumoniae. Microorganism-antibiotic combinations that gave very major errors were CNS-erythromycin, CNS-oxacillin, enterococci-teicoplanin, and enterococci-high-concentration gentamicin. Major errors were observed for CNS-oxacillin and S. agalactiae-tetracycline combinations. In conclusion the results of this study indicate that the VITEK 2 system represents an accurate and acceptable means for performing identification and antibiotic susceptibility tests with medically relevant gram-positive cocci.
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Affiliation(s)
- Marco Ligozzi
- Sezione di Microbiologia, Dipartimento di Patologia, Università di Verona, Strada le Grazie 8, 35100 Verona, Italy
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40
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Nedoluha PC, Owens S, Russek-Cohen E, Westhoff DC. Effect of sampling method on the representative recovery of microorganisms from the surfaces of aquacultured finfish. J Food Prot 2001; 64:1515-20. [PMID: 11601699 DOI: 10.4315/0362-028x-64.10.1515] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The objective of this study was to determine if a gentle rinse procedure was equivalent to the combination of excision and homogenization with a stomacher for the relative removal of various microorganisms from finfish fillets. Fillets of hybrid striped bass and rainbow trout were obtained from local markets and sampled using three methods: rinse (R), excision followed by homogenization in a stomacher (S), and homogenization of fillets following a rinse (RS). Microorganisms were enumerated on selective and nonselective media, and randomly selected colonies from aerobic plate counts were identified using MIDI Sherlock and BIOLOG microbial identification systems. Enrichments and selective media were used for the isolation of Listeria monocytogenes, Salmonella spp., and Yersinia enterocolitica. This study confirms previous reports that stomaching is superior to rinsing for enumerating total microbial populations from fish fillets. Rinsing was more effective for rainbow trout than for striped bass. Sampling method did not affect the relative magnitude of plate counts on media selective for aeromonads, pseudomonads, Shewanella, lactic acid bacteria, enterics, and gram-positive cocci. In the compositional analysis of random isolates, R recovered significantly lower fractions of aeromonads than did S or RS, but sampling method did not affect the percent recovery of lactic acid bacteria, pseudomonads, Shewanella, Moraxellaceae, or Cytophaga/Flavobacterium. However, observations suggest that with increased replication, differences among Moraxellaceae, Pseudomonas, and gram positives might be significant. Only one L. monocytogenes colony was isolated, and no Salmonella or Y. enterocolitica, so the effect of sampling method could not be determined for these organisms. Differences in predominant bacterial populations were seen between fish species.
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Affiliation(s)
- P C Nedoluha
- University of Maryland, Department of Animal and Avian Sciences, College Park 20770, USA
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41
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Joyanes P, del Carmen Conejo M, Martínez-Martínez L, Perea EJ. Evaluation of the VITEK 2 system for the identification and susceptibility testing of three species of nonfermenting gram-negative rods frequently isolated from clinical samples. J Clin Microbiol 2001; 39:3247-53. [PMID: 11526158 PMCID: PMC88326 DOI: 10.1128/jcm.39.9.3247-3253.2001] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
VITEK 2 is a new automatic system for the identification and susceptibility testing of the most clinically important bacteria. In the present study 198 clinical isolates, including Pseudomonas aeruginosa (n = 146), Acinetobacter baumannii (n = 25), and Stenotrophomonas maltophilia (n = 27) were evaluated. Reference susceptibility testing of cefepime, cefotaxime, ceftazidime, ciprofloxacin, gentamicin, imipenem, meropenem, piperacillin, tobramycin, levofloxacin (only for P. aeruginosa), co-trimoxazole (only for S. maltophilia), and ampicillin-sulbactam and tetracycline (only for A. baumannii) was performed by microdilution (NCCLS guidelines). The VITEK 2 system correctly identified 91.6, 100, and 76% of P. aeruginosa, S. maltophilia, and A. baumannii isolates, respectively, within 3 h. The respective percentages of essential agreement (to within 1 twofold dilution) for P. aeruginosa and A. baumannii were 89.0 and 88.0% (cefepime), 91.1 and 100% (cefotaxime), 95.2 and 96.0% (ceftazidime), 98.6 and 100% (ciprofloxacin), 88.4 and 100% (gentamicin), 87.0 and 92.0% (imipenem), 85.0 and 88.0% (meropenem), 84.2 and 96.0% (piperacillin), and 97.3 and 80% (tobramycin). The essential agreement for levofloxacin against P. aeruginosa was 86.3%. The percentages of essential agreement for ampicillin-sulbactam and tetracycline against A. baumannii were 88.0 and 100%, respectively. Very major errors for P. aeruginosa (resistant by the reference method, susceptible with the VITEK 2 system [resistant to susceptible]) were noted for cefepime (0.7%), cefotaxime (0.7%), gentamicin (0.7%), imipenem (1.4%), levofloxacin (2.7%), and piperacillin (2.7%) and, for one strain of A. baumannii, for imipenem. Major errors (susceptible to resistant) were noted only for P. aeruginosa and cefepime (2.0%), ceftazidime (0.7%), and piperacillin (3.4%). Minor errors ranged from 0.0% for piperacillin to 22.6% for cefotaxime against P. aeruginosa and from 0.0% for piperacillin and ciprofloxacin to 20.0% for cefepime against A. baumannii. The VITEK 2 system provided co-trimoxazole MICs only for S. maltophilia; no very major or major errors were obtained for co-trimoxazole against this species. It is concluded that the VITEK 2 system allows the rapid identification of S. maltophilia and most P. aeruginosa and A. baumannii isolates. The VITEK 2 system can perform reliable susceptibility testing of many of the antimicrobial agents used against P. aeruginosa and A. baumannii. It would be desirable if new versions of the VITEK 2 software were able to determine MICs and the corresponding clinical categories of agents active against S. maltophilia.
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Affiliation(s)
- P Joyanes
- Department of Microbiology, School of Medicine, University of Seville, Seville, Spain
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42
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Freydiere AM, Guinet R, Boiron P. Yeast identification in the clinical microbiology laboratory: phenotypical methods. Med Mycol 2001; 39:9-33. [PMID: 11270413 DOI: 10.1080/mmy.39.1.9.33] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Emerging yeast pathogens are favoured by increasing numbers of immunocompromised patients and by certain current medical practices. These yeasts differ in their antifungal drug susceptibilities, and rapid species identification is imperative. A large variety of methods have been developed with the aim of facilitating rapid, accurate yeast identification. Significant recent commercial introductions have included species-specific direct enzymatic colour tests, differential chromogenic isolation plates, direct immunological tests, and enhanced manual and automated biochemical and enzymatic panels. Chromogenic isolation media demonstrate better detection rates of yeasts in mixed cultures than traditional media, and allow the direct identification of Candida albicans by means of colony colour. Comparative evaluation of rapid methods for C. albicans identification, including the germ tube test, shows that chromogenic media may be economically advantageous. Accurate tests for single species include the Bichrolatex Albicans and Krusei Color tests, both immunologically based, as well as the Remel Rapid Trehalose Assimilation Broth for C. glabrata. Among broad-spectrum tests, the RapID Yeast Plus system gives same-day identification of clinical yeasts, but performance depends on inoculum density and geographic isolate source. The API 20 C AUX system is considered a reference method, but newer systems such as Auxacolor and Fungichrom are as accurate and are more convenient. Among automated systems, the ID 32 C strip, the Vitek Yeast Biochemical Card and the Vitek 2 ID-YST system correctly identify >93% of common yeasts, but the ID-YST is the most accurate with uncommon yeasts, including C. dubliniensis. Spectroscopic methods such as Fourier transformed-infrared spectroscopy offer potential advantages for the future. Overall, the advantages of rapid yeast identification methods include relative simplicity and low cost. For all rapid methods, meticulous, standardized multicenter comparisons are needed before tests are fully accepted.
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Affiliation(s)
- A M Freydiere
- Laboratoire de Microbiologie, H pital de l'Antiquaille, Lyon, France.
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43
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Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP, Raoult D. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 2000; 38:3623-30. [PMID: 11015374 PMCID: PMC87447 DOI: 10.1128/jcm.38.10.3623-3630.2000] [Citation(s) in RCA: 636] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Some bacteria are difficult to identify with phenotypic identification schemes commonly used outside reference laboratories. 16S ribosomal DNA (rDNA)-based identification of bacteria potentially offers a useful alternative when phenotypic characterization methods fail. However, as yet, the usefulness of 16S rDNA sequence analysis in the identification of conventionally unidentifiable isolates has not been evaluated with a large collection of isolates. In this study, we evaluated the utility of 16S rDNA sequencing as a means to identify a collection of 177 such isolates obtained from environmental, veterinary, and clinical sources. For 159 isolates (89.8%) there was at least one sequence in GenBank that yielded a similarity score of > or =97%, and for 139 isolates (78.5%) there was at least one sequence in GenBank that yielded a similarity score of > or =99%. These similarity score values were used to defined identification at the genus and species levels, respectively. For isolates identified to the species level, conventional identification failed to produce accurate results because of inappropriate biochemical profile determination in 76 isolates (58.7%), Gram staining in 16 isolates (11.6%), oxidase and catalase activity determination in 5 isolates (3.6%) and growth requirement determination in 2 isolates (1.5%). Eighteen isolates (10.2%) remained unidentifiable by 16S rDNA sequence analysis but were probably prototype isolates of new species. These isolates originated mainly from environmental sources (P = 0.07). The 16S rDNA approach failed to identify Enterobacter and Pantoea isolates to the species level (P = 0.04; odds ratio = 0.32 [95% confidence interval, 0.10 to 1.14]). Elsewhere, the usefulness of 16S rDNA sequencing was compromised by the presence of 16S rDNA sequences with >1% undetermined positions in the databases. Unlike phenotypic identification, which can be modified by the variability of expression of characters, 16S rDNA sequencing provides unambiguous data even for rare isolates, which are reproducible in and between laboratories. The increase in accurate new 16S rDNA sequences and the development of alternative genes for molecular identification of certain taxa should further improve the usefulness of molecular identification of bacteria.
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Affiliation(s)
- M Drancourt
- Laboratoire de Microbiologie, Centre Hospitalier Universitaire La Timone, Marseille, France
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44
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Marano NN, Daniels NA, Easton AN, McShan A, Ray B, Wells JG, Griffin PM, Angulo FJ. A survey of stool culturing practices for vibrio species at clinical laboratories in Gulf Coast states. J Clin Microbiol 2000; 38:2267-70. [PMID: 10834987 PMCID: PMC86778 DOI: 10.1128/jcm.38.6.2267-2270.2000] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Non-cholera Vibrio infections are an important public health problem. Non-cholera Vibrio species usually cause sporadic infections, often in coastal states, and have also caused several recent nationwide outbreaks of gastroenteritis in the United States. We report a survey of laboratory stool culturing practices for Vibrio among randomly selected clinical laboratories in Gulf Coast states (Alabama, Florida, Louisiana, Mississippi, and Texas). Interviews conducted with the microbiology supervisors of 201 clinical laboratories found that 164 (82%) received stool specimens for culture. Of these, 102 (62%) of 164 processed stool specimens on site, and 20 (20%) of these 102 laboratories cultured all stool specimens for Vibrio, indicating that at least 34,463 (22%) of 152, 797 stool specimens were cultured for Vibrio. This survey suggests that despite an increased incidence of non-cholera Vibrio infections in Gulf Coast states, a low percentage of clinical laboratories routinely screen all stool specimens, and fewer than 25% of stool specimens collected are routinely screened for non-cholera Vibrio.
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Affiliation(s)
- N N Marano
- Foodborne and Diarrheal Diseases Branch, Division of Bacterial and Mycotic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
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Cantón R, Pérez-Vázquez M, Oliver A, Sánchez Del Saz B, Gutiérrez MO, Martínez-Ferrer M, Baquero F. Evaluation of the Wider system, a new computer-assisted image-processing device for bacterial identification and susceptibility testing. J Clin Microbiol 2000; 38:1339-46. [PMID: 10747104 PMCID: PMC86442 DOI: 10.1128/jcm.38.4.1339-1346.2000] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/1999] [Accepted: 01/10/2000] [Indexed: 11/20/2022] Open
Abstract
The Wider system is a newly developed computer-assisted image-processing device for both bacterial identification and antimicrobial susceptibility testing. It has been adapted to be able to read and interpret commercial MicroScan panels. Two hundred forty-four fresh consecutive clinical isolates (138 isolates of the family Enterobacteriaceae, 25 nonfermentative gram-negative rods [NFGNRs], and 81 gram-positive cocci) were tested. In addition, 100 enterobacterial strains with known beta-lactam resistance mechanisms (22 strains with chromosomal AmpC beta-lactamase, 8 strains with chromosomal class A beta-lactamase, 21 broad-spectrum and IRT beta-lactamase-producing strains, 41 extended-spectrum beta-lactamase-producing strains, and 8 permeability mutants) were tested. API galleries and National Committee for Clinical Laboratory Standards (NCCLS) microdilution methods were used as reference methods. The Wider system correctly identified 97.5% of the clinical isolates at the species level. Overall essential agreement (+/-1 log(2) dilution for 3,719 organism-antimicrobial drug combinations) was 95.6% (isolates of the family Enterobacteriaceae, 96.6%; NFGNRs, 88.0%; gram-positive cocci, 95.6%). The lowest essential agreement was observed with Enterobacteriaceae versus imipenem (84.0%), NFGNR versus piperacillin (88.0%) and cefepime (88.0%), and gram-positive isolates versus penicillin (80.4%). The category error rate (NCCLS criteria) was 4.2% (2.0% very major errors, 0.6% major errors, and 1. 5% minor errors). Essential agreement and interpretive error rates for eight beta-lactam antibiotics against isolates of the family Enterobacteriaceae with known beta-lactam resistance mechanisms were 94.8 and 5.4%, respectively. Interestingly, the very major error rate was only 0.8%. Minor errors (3.6%) were mainly observed with amoxicillin-clavulanate and cefepime against extended-spectrum beta-lactamase-producing isolates. The Wider system is a new reliable tool which applies the image-processing technology to the reading of commercial trays for both bacterial identification and susceptibility testing.
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Affiliation(s)
- R Cantón
- Servicio de Microbiología, Hospital Ramón y Cajal, Madrid 28034, Spain.
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46
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Ivnitski D, Abdel-Hamid I, Atanasov P, Wilkins E, Stricker S. Application of Electrochemical Biosensors for Detection of Food Pathogenic Bacteria. ELECTROANAL 2000. [DOI: 10.1002/(sici)1521-4109(20000301)12:5<317::aid-elan317>3.0.co;2-a] [Citation(s) in RCA: 140] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Ivnitski D, Abdel-Hamid I, Atanasov P, Wilkins E. Biosensors for detection of pathogenic bacteria. Biosens Bioelectron 1999. [DOI: 10.1016/s0956-5663(99)00039-1] [Citation(s) in RCA: 420] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tang YW, Ellis NM, Hopkins MK, Smith DH, Dodge DE, Persing DH. Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli. J Clin Microbiol 1998; 36:3674-9. [PMID: 9817894 PMCID: PMC105261 DOI: 10.1128/jcm.36.12.3674-3679.1998] [Citation(s) in RCA: 199] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid and accurate identification of bacterial pathogens is a fundamental goal of clinical microbiology, but one that is difficult or impossible for many slow-growing and fastidious organisms. We used identification systems based on cellular fatty acid profiles (Sherlock; MIDI, Inc., Newark, Del.), carbon source utilization (Microlog; Biolog, Inc., Hayward, Calif.), and 16S rRNA gene sequence (MicroSeq; Perkin-Elmer Applied Biosystems Division, Foster City, Calif.) to evaluate 72 unusual aerobic gram-negative bacilli isolated from clinical specimens at the Mayo Clinic. Compared to lengthy conventional methods, Sherlock, Microlog, and MicroSeq were able to identify 56 of 72 (77.8%), 63 of 72 (87.5%), and 70 of 72 (97.2%) isolates to the genus level (P = 0.002) and 44 to 65 (67.7%), 55 of 65 (84.6%), and 58 of 65 (89.2%) isolates to the species level (P = 0.005), respectively. Four Acinetobacter and three Bordetella isolates which could not be identified to the species level by conventional methods were identified by MicroSeq. In comparison to the full 16S rDNA sequences, the first 527 bp provided identical genus information for all 72 isolates and identical species information for 67 (93.1%) isolates. These data show that MicroSeq provides rapid, unambiguous identification of clinical bacterial isolates. The improved turnaround time provided by genotypic identification systems may translate into improved clinical outcomes.
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Affiliation(s)
- Y W Tang
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
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Richardson H, Smaill F. Recent advances: medical microbiology. BMJ (CLINICAL RESEARCH ED.) 1998; 317:1060-2. [PMID: 9774296 PMCID: PMC1114065 DOI: 10.1136/bmj.317.7165.1060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- H Richardson
- Divisions of Medical Microbiology and Infectious Diseases, Departments of Pathology and Medicine, Faculty of Health Science, McMaster University, Hamilton, Ontario, Canada L8N 3Z5.
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Funke G, Monnet D, deBernardis C, von Graevenitz A, Freney J. Evaluation of the VITEK 2 system for rapid identification of medically relevant gram-negative rods. J Clin Microbiol 1998; 36:1948-52. [PMID: 9650942 PMCID: PMC104958 DOI: 10.1128/jcm.36.7.1948-1952.1998] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The new VITEK 2 system (bioMérieux) was evaluated at two independent sites with the identification card for gram-negative bacilli (ID-GNB card). Of the 845 strains tested, which represented 70 different taxa belonging to either the family Enterobacteriaceae or the nonenteric bacilli, 716 (84.7%) were correctly identified at the species level. Thirty-two (3.8%) additional strains were identified to the species level after the performance of simple, rapid manual tests (oxidase, hemolysis, indole reaction, motility, and pigmentation). For 80 (9.5%) strains, these additional tests did not lead to an identification at the species level but the correct species identification was given among the organisms listed. Only 7 (0.8%) strains were misidentified, and 10 (1.2%) were not identified. Mistakes were randomly distributed over different taxa. Due to the new, more sensitive fluorescence-based technology of the VITEK 2 system, final results were available after 3 h. Since our evaluation was mainly a stress test, it is predicted that the VITEK 2 system in conjunction with the ID-GNB card would perform well under conditions of a routine clinical laboratory in identifying members of the family Enterobacteriaceae and selected species of nonenteric bacteria. This system is a promising, highly automated new tool for the rapid identification of gram-negative bacilli from human clinical specimens.
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Affiliation(s)
- G Funke
- Department of Medical Microbiology, University of Zürich, Switzerland.
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