scholarly journals Usefulness of the MicroSeq 500 16S rDNA bacterial identification system for identification of anaerobic Gram positive bacilli isolated from blood cultures

2006 ◽  
Vol 59 (2) ◽  
pp. 219-222 ◽  
Author(s):  
S K P Lau
Keyword(s):  
16S Rdna ◽  
Blood Cultures ◽  
Identification System ◽  
Bacterial Identification ◽  
Gram Positive

scholarly journals First Report of Crown Gall, Caused by Agrobacterium tumefaciens on Soapberry (Sapindus delavayi) in China

Plant Disease ◽  
2013 ◽  
Vol 97 (5) ◽  
pp. 685-685
Author(s):  
Y. J. Wang ◽  
Y. Y. He ◽  
Z. Xie ◽  
L. Q. Zhang
Keyword(s):  
Agrobacterium Tumefaciens ◽  
16S Rdna ◽  
Crown Gall ◽  
Maximum Parsimony Analysis ◽  
Bacterial Suspension ◽  
Identification System ◽  
Distilled Water ◽  
Bacterial Identification ◽  
Poor Growth ◽  
First Report

Soapberry (Sapindus delavayi (Franch.) Radlk.,) plants are widely grown as shade trees in the subtropical to tropical regions of China. In July 2011, large, aerial galls were observed on the above-ground trunks of 5-year-old soapberry plants in two commercial nursery gardens located in Zhejiang Province. Disease incidence was estimated to be 75%. The galls varied in weight from 2 to 24 g and in texture from soft and spongy to hard, and in some cases, the galls completely girdled the trunk. The trees with galls exhibited poor growth compared with healthy trees. Isolations from the grinded and macerated galls yielded nearly pure white, circular, and glistening bacterial colonies on Roy Sauer medium (2). Six random colonies from different galls were selected for bacterial identification, and showed the same morphological, physiological, and biochemical characters and 16S rDNA sequences. All six isolates (isolate SD01 to SD06) were gram negative, rod-shaped bacteria. Carbon source utilization testing with the Biolog GN Bacterial Identification System (version 3.50) confirmed the bacteria as Agrobacterium tumefaciens with a similarity of 0.90. The most-parsimonious tree from the maximum parsimony analysis (PHYLIP package, version 3.68, 500 replicates) of bacterial 16S rDNA gene sequences showed that A. tumefaciens SD01 (GenBank Accession No. JX997939) clustered phylogenetically most closely (99.5% similarity) with A. tumefaciens C58 (AE007870.2). Pathogenicity was confirmed by injecting 3- to 5-week old tomato and sunflower plants and 2-year-old soapberry with approximately 5 μl of the bacterial suspension (108 CFU/ml) in sterile, distilled water. Sterile distilled water was used as a negative control. Ten plants of each treatment were inoculated. Inoculated plants were then transferred to a greenhouse at 25°C. Typical tumors developed at the inoculation sites on tomatoes and sunflower plants 3 weeks after inoculation and on soapberry 6 weeks after inoculation. No symptoms were observed on the control plants. The bacteria that were readily reisolated from the inoculated plants exhibited the same morphological, physiological characters and 16S rDNA sequence as the original culture and were confirmed as A. tumefaciens, fulfilling Koch's postulates. A. tumefaciens is endemic to China and has a very wide host range (1). However, crown gall of soapberry has never been found in China and other countries. To our knowledge, this is the first report of A. tumefaciens on soapberry plants in China. References: (1) M. A. Escobar and A. M. Dandekar. Trends Plant Sci. 8:380, 2003. (2) L. W. Moore et al. Page 17 in: Laboratory Guide for Identification of Plant Pathogenic Bacteria. 3rd ed. N. W. Schaad et al., eds. The American Phytopathological Society, St. Paul, MN, 2001.

scholarly journals Sequence-Based Identification of Mycobacterium Species Using the MicroSeq 500 16S rDNA Bacterial Identification System

2000 ◽  
Vol 38 (1) ◽  
pp. 246-251
Author(s):  
Jean Baldus Patel ◽  
Debra G. B. Leonard ◽  
Xai Pan ◽  
James M. Musser ◽  
Richard E. Berman ◽  
...  
Keyword(s):  
16S Rdna ◽  
High Performance ◽  
Identification System ◽  
Bacterial Identification ◽  
Phenotypic Analysis ◽  
16S Rdna Sequence ◽  
Mycolic Acids ◽  
Phenotypic Identification ◽  
Gene Sequence Analysis ◽  
Phenotypic Methods

ABSTRACT We evaluated the MicroSeq 500 16S rDNA Bacterial Sequencing Kit (PE Applied Biosystems), a 500-bp sequence-based identification system, for its ability to identify clinical Mycobacterium isolates. The organism identity was determined by comparing the 16S rDNA sequence to the MicroSeq database, which consists primarily of type strain sequences. A total of 113 isolates (18 different species), previously recovered and identified by routine methods from two clinical laboratories, were analyzed by the MicroSeq method. Isolates with discordant results were analyzed by hsp65 gene sequence analysis and in some cases repeat phenotypic identification, AccuProbe rRNA hybridization (Gen-Probe, Inc., San Diego, Calif.), or high-performance liquid chromatography of mycolic acids. For 93 (82%) isolates, the MicroSeq identity was concordant with the previously reported identity. For 18 (16%) isolates, the original identification was discordant with the MicroSeq identification. Of the 18 discrepant isolates, 7 (six unique sequences) were originally misidentified by phenotypic analysis or the AccuProbe assay but were correctly identified by the MicroSeq assay. Of the 18 discrepant isolates, 11 (seven unique sequences) were unusual species that were difficult to identify by phenotypic methods and, in all but one case, by molecular methods. The remaining two isolates (2%) failed definitive phenotypic identification, but the MicroSeq assay was able to definitively identify one of these isolates. The MicroSeq identification system is an accurate and rapid method for the identification of Mycobacterium spp.

Assessment of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF- MS) for Accurate Bacterial Identification in Clinical Labs

2020 ◽  
Vol 154 (Supplement_1) ◽  
pp. S143-S143
Author(s):  
M Abdel-Rahman ◽  
M S Azab ◽  
M Meibed ◽  
A El-Kholy ◽  
A W Elmetwalli
Keyword(s):  
Blood Cultures ◽  
Bacterial Identification ◽  
Gram Positive ◽  
Gram Negative ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Identification Of Bacteria ◽  
Vitek 2 ◽  
Phenotypic Methods ◽  
Tof Ms

Abstract Introduction/Objective On behalf of the diagnostic Medical Laboratory rapid, and accurate identification of bacteria with their one-to-one anti-microbial susceptibility outlines is of ultimate importance for the management of infected patients. Contemporary microbial identification methods employed in routine clinical diagnostic laboratories relies on the use of conventional phenotypic methods. Phenotypic methods are time consuming with minimum turn-around times of at least 24 hrs and in many occurrences of 48hrs. With the intention of accelerate laboratory processes the MALDI-TOF MS was familiarized. MALDI-TOF MS is established on proteomic profiling and permits for rapid identification of bacteria. This technology has not been widely used in Egypt, but has been regularly used in Europe for the past few years. Methods Two hundred forty three positive non duplicate blood cultures were accrued over a period of six months. Experimental aliquots were taken from excess sample material that was collected as part of routine clinical care. 105 were positive for Gram negative bacilli, 123 were positive for Gram positive cocci, 3 positive for Gram positive bacilli, and 7 were positive for yeast. MALDI-TOF identification was compared to conventional identification. Conventional identification consisted of a combination of MALDI-TOF identification of a subcultures colony by direct smear, biochemical reactions, Vitek 2, and molecular identification. Results Ninety seven of the one hundred and five blood cultures positive for Gram negative bacilli were monomicrobial. The majority of these were identified as Escherichia coli by conventional methods, followed by Klebsiella pneumoniae and Pseudomonas aeruginosa. Eighty-four of these monomicrobial cultures were identified by MALDI-TOF to the species level. Eighty-one of the eighty-four were concordant with the conventional identification (96.4%). Conclusion The MALDI-TOF proved to be useful for the rapid and reliable identification of g-ve bacteria from the clinical specimens. The difference in turnaround time for bacterial identification was significant between MALDI-TOF MS and VITEK 2 with minimal preparation for the blood cultures.

Rapid demonstration of septic or infectious arthritis due to Gram-negative bacteria

1992 ◽  
Vol 50 (1) ◽  
pp. 686-687
Author(s):  
Jacob S. Hanker ◽  
Paul R. Gross ◽  
Beverly L. Giammara
Keyword(s):  
Chronic Arthritis ◽  
Blood Cultures ◽  
Gram Negative Bacteria ◽  
Infectious Arthritis ◽  
Bacterial Arthritis ◽  
Gram Positive ◽  
Gram Negative ◽  
Gram Positive Bacteria

Blood cultures are positive in approximately only 50 per cent of the patients with nongonococcal bacterial infectious arthritis and about 20 per cent of those with gonococcal arthritis. But the concept that gram-negative bacteria could be involved even in chronic arthritis is well-supported. Gram stains are more definitive in staphylococcal arthritis caused by gram-positive bacteria than in bacterial arthritis due to gram-negative bacteria. In the latter situation where gram-negative bacilli are the problem, Gram stains are helpful for 50% of the patients; they are only helpful for 25% of the patients, however, where gram-negative gonococci are the problem. In arthritis due to gram-positive Staphylococci. Gramstained smears are positive for 75% of the patients.

The Causative Organisms of Bacterial Meningitis and their Antimicrobial Resistance Profiles in Iranian Children in 2011-2016

2020 ◽  
Vol 20 (2) ◽  
pp. 229-236
Author(s):  
Sepideh Keshavarz Valian ◽  
Shima Mahmoudi ◽  
Babak Pourakbari ◽  
Maryam Banar ◽  
Mohammad Taghi Haghi Ashtiani ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Bacterial Meningitis ◽  
Medical Center ◽  
Blood Cultures ◽  
Gram Positive ◽  
Gram Negative ◽  
Number Of Patients ◽  
Resistance Patterns ◽  
Iranian Children ◽  
Surgery Department

Objective: The study aimed to describe the identity and antimicrobial resistance patterns of the causative agents of bacterial meningitis in children referred to Children’s Medical Center (CMC) Hospital, Tehran, Iran. Methods: This retrospective study was performed at CMC Hospital during a six-year period from 2011 to 2016. The microbiological information of the patients with a diagnosis of bacterial meningitis was collected and the following data were obtained: patients’ age, sex, hospital ward, the results of CSF and blood cultures, and antibiotic susceptibility profiles of isolated organisms. Results: A total of 118 patients with bacterial meningitis were admitted to CMC hospital. Sixty-two percent (n=73) of the patients were male. The median age of the patients was ten months (interquartile range [IQR]: 2 months-2 years) and the majority of them (n=92, 80%) were younger than two years of age. The highest number of patients (n=47, 40%) were admitted to the surgery department. Streptococcus epidermidis was the most frequent isolated bacterium (n=27/127, 21%), followed by Klebsiella pneumoniae (n=20/127, 16%), and Staphylococcus aureus (n=16/127, 12.5%). Blood culture was positive in 28% (n=33/118) of patients. Ampicillin-sulbactam and imipenem were the most effective antibiotics against Gram-negative bacteria isolated from CSF cultures. In the case of Gram-positive organisms, ampicillinsulbactam, vancomycin, and linezolid were the best choices. Imipenem was the most active drug against Gram-negative blood pathogens. Also, ampicillin and vancomycin had the best effect on Gram-positive bacteria isolated from blood cultures. Conclusion: Results of this study provide valuable information about the antibiotic resistance profiles of the etiologic agents of childhood meningitis, which can be used for prescription of more effective empirical therapies.

scholarly journals Evaluation of MicroScan Bacterial Identification Panels for Low-Resource Settings

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 349
Author(s):  
Sien Ombelet ◽  
Alessandra Natale ◽  
Jean-Baptiste Ronat ◽  
Olivier Vandenberg ◽  
Liselotte Hardy ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Ease Of Use ◽  
Bacterial Identification ◽  
Gram Positive ◽  
Gram Negative ◽  
Low Resource Settings ◽  
Low Resource ◽  
Bacillus Spp ◽  
Gram Negative Organisms ◽  
Instructions For Use

Bacterial identification is challenging in low-resource settings (LRS). We evaluated the MicroScan identification panels (Beckman Coulter, Brea, CA, USA) as part of Médecins Sans Frontières’ Mini-lab Project. The MicroScan Dried Overnight Positive ID Type 3 (PID3) panels for Gram-positive organisms and Dried Overnight Negative ID Type 2 (NID2) panels for Gram-negative organisms were assessed with 367 clinical isolates from LRS. Robustness was studied by inoculating Gram-negative species on the Gram-positive panel and vice versa. The ease of use of the panels and readability of the instructions for use (IFU) were evaluated. Of species represented in the MicroScan database, 94.6% (185/195) of Gram-negative and 85.9% (110/128) of Gram-positive isolates were correctly identified up to species level. Of species not represented in the database (e.g., Streptococcus suis and Bacillus spp.), 53.1% out of 49 isolates were incorrectly identified as non-related bacterial species. Testing of Gram-positive isolates on Gram-negative panels and vice versa (n = 144) resulted in incorrect identifications for 38.2% of tested isolates. The readability level of the IFU was considered too high for LRS. Inoculation of the panels was favorably evaluated, whereas the visual reading of the panels was considered error-prone. In conclusion, the accuracy of the MicroScan identification panels was excellent for Gram-negative species and good for Gram-positive species. Improvements in stability, robustness, and ease of use have been identified to assure adaptation to LRS constraints.

scholarly journals Evaluation of the LightCycler Staphylococcus MGRADE Kits on Positive Blood Cultures That Contained Gram-Positive Cocci in Clusters

2005 ◽  
Vol 43 (12) ◽  
pp. 6144-6146 ◽  
Author(s):  
N. K. Shrestha ◽  
M. J. Tuohy ◽  
R. A. Padmanabhan ◽  
G. S. Hall ◽  
G. W. Procop
Keyword(s):  
Blood Cultures ◽  
Gram Positive ◽  
Gram Positive Cocci

scholarly journals Evaluation of MRSASelect™Chromogenic Medium for the Early Detection of Methicillin-ResistantStaphylococcus aureusfrom Blood Cultures

2013 ◽  
Vol 24 (4) ◽  
pp. e113-e116 ◽  
Author(s):  
Kanchana Manickam ◽  
Andrew Walkty ◽  
Philippe RS Lagacé-Wiens ◽  
Heather Adam ◽  
Barbara Swan ◽  
...  
Keyword(s):  
Early Detection ◽  
Antimicrobial Therapy ◽  
Predictive Value ◽  
Turnaround Time ◽  
Blood Cultures ◽  
Gram Stain ◽  
Chromogenic Medium ◽  
Gram Positive ◽  
Microbiological Methods ◽  
Gram Positive Cocci

INTRODUCTION:Staphylococcus aureusbacteremia is associated with considerable morbidity and mortality. In theory, reducing the turnaround time in reporting of methicillin-resistantS aureus(MRSA) among patients with bactermia could assist with the rapid optimization of antimicrobial therapy.OBJECTIVE: To evaluate the sensitivity and specificity of MRSASelect(Bio-Rad Laboratories, USA), a chromogenic medium, in the early detection of MRSA from blood cultures growing Gram-positive cocci in clusters, and to confirm that routine use of this medium would, in fact, reduce turnaround time for MRSA identification.METHODS: The present study was conducted at three microbiology laboratories in Manitoba. Between April 2010 and May 2011, positive blood cultures with Gram-positive cocci in clusters visualized on Gram stain were subcultured to both MRSASelectand routine media. MRSA isolates were identified using conventional microbiological methods from routine media and using growth with the typical colony morphology (pink colony) on MRSASelectmedium.RESULTS: A total of 490 blood cultures demonstrating Gram-positive cocci in clusters on Gram stain were evaluated.S aureuswas recovered from 274 blood cultures, with 51S aureusisolates (51 of 274 [18.6%]) identified as MRSA. MRSASelectmedium had a sensitivity of 98%, a specificity of 100%, a positive predictive value of 100% and a negative predictive value of 99.8% for the recovery and identification of MRSA directly from positive blood culture bottles. In addition, use of MRSASelectmedium was found to improve turnaround time in the detection of MRSA by almost 24 h relative to conventional methods.DISCUSSION: These data support the utility of MRSASelectmedium for the rapid identification of MRSA from positive blood cultures. Further clinical studies are warranted to determine whether the improvement in turnaround time will result in a measurable reduction in suboptimal antimicrobial therapy and/or improvement in patient outcome.

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