scholarly journals The development and assessment of a bacteriocin typing method forKlebsiella

1979 ◽  
Vol 82 (2) ◽  
pp. 207-223 ◽  
Author(s):  
A. S. Edmondson ◽  
E. Mary Cooke
Keyword(s):  
Close Agreement ◽  
Reliable Method ◽  
Natural Populations ◽  
Good Discrimination ◽  
Typing Method ◽  
Acceptable Accuracy ◽  
Cultural Conditions ◽  
Typing Methods ◽  
Complete Set ◽  
Bacteriocin Typing

SUMMARYKlebsiellas are generally typed by the method of capsular serotyping but, although this is a reliable method, it is time consuming, requires the production of a large number of antisera and is not generally available. For this reason another method for typing klebsiellas was sought.A bacteriocin typing method involving mitomycin C induction was developed and the cultural conditions giving optimum klebecin production and the best methods of testing the sensitivity of the organisms to klebecins were determined.Of 190 klebsiella strains screened for bacteriocinogeny, only 68 (35·8%) produced klebecin and after calculation of similarity values by computer analysis, a typing set of 15 producers was selected. This typing set allowed over 96% of klebsiella strains to be typed and tests of the reproducibility of the method and the variability of typing patterns in natural populations of klebsiella indicated that results of acceptable accuracy could be obtained, while retaining good discrimination if two or more differences were required between patterns before they were regarded as distinct.A complete set of capsular antisera were prepared, enabling the results obtained from klebecin typing to be compared with those from serotyping. There was generally close agreement between the results from the two typing methods and greater discrimination was obtained between similar strains when the two methods were combined. Klebecin typing and serotyping revealed relationships between strains from five outbreaks of infection, and strains of the same serotype from different hospitals could frequently be distinguished by their klebecin typing patterns.

The phylogenetic analysis of Dalbergia (Fabaceae: Papilionaceae) based on different DNA barcodes

Holzforschung ◽  
2017 ◽  
Vol 71 (12) ◽  
pp. 939-949 ◽  
Author(s):  
Qiwei Li ◽  
Jihong Wu ◽  
Yesheng Wang ◽  
Xiaoming Lian ◽  
Feilong Wu ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Reliable Method ◽  
Dna Barcodes ◽  
Illegal Logging ◽  
Good Discrimination ◽  
Close Match ◽  
Discrimination Ability ◽  
Overall Performance ◽  
Resources Conservation ◽  
Barcode Gap

AbstractThe genusDalbergiacontains approximately 250 species with many valuable trees being destroyed by targeted and illegal logging. DNA barcoding is a reliable method for the molecular identification of different species and resources conservation. In the present study, the specimen discrimination ability of internal transcribed spacer (ITS),matK,rbcL andpsbA-trnH barcoding were tested onDalbergiasequences, downloaded from the National Center for Biotechnology Information (NCBI), and the combined barcoding ITS+matK+rbcL was used to identify unknown specimens. It was found that ITS+matK+rbcL have good discrimination rates based on the analysis methods best match (BM) and best close match (BCM). These barcodes also have the best performance concerning barcode gap distribution, and are able to discriminate unknown specimens from South-China. Furthermore, it was demonstrated thatD. tamarindifoliaandD. rubiginosaare also relatively close to sister-speciesD. pinnataandD. candenatensiswithin the phylogeneticDalbergiatree. Considering the overall performance of these barcodes, we suggest that the ITS+matK+rbcL region is a suitable barcode for identifyingDalbergiaspecies.

Potential of Three-Way Randomly Amplified Polymorphic DNA Analysis as a Typing Method for TwelveSalmonella Serotypes

1999 ◽  
Vol 65 (11) ◽  
pp. 4830-4836 ◽  
Author(s):  
S. M. Soto ◽  
B. Guerra ◽  
M. A. González-Hevia ◽  
M. C. Mendoza
Keyword(s):  
Dna Analysis ◽  
Phage Typing ◽  
Clinical Samples ◽  
Randomly Amplified Polymorphic Dna ◽  
Typing Method ◽  
Phage Types ◽  
Typing Methods ◽  
In Vitro Stability ◽  
Reference Strains

ABSTRACT The potential of a three-way randomly amplified polymorphic DNA (RAPD) procedure (RAPD typing) for typing Salmonella enterica strains assigned to 12 serotypes was analyzed. The series of organisms used included 235 strains (326 isolates) collected mainly from clinical samples in the Principality of Asturias and 9 reference strains. RAPD typing was performed directly with broth cultures of bacteria by using three selected primers and optimized PCR conditions. The profiles obtained with the three primers were used to define RAPD types and to evaluate the procedure as a typing method at the species and serotype levels. The typeability was 100%; the reproducibility and in vitro stability could be considered good. The concordance of RAPD typing methods with serotyping methods was 100%, but some profiles obtained with two of the three primers were obtained with strains assigned to different serotypes. The discrimination index (DI) within the series of organisms was 0.94, and the DI within serotypes Typhimurium, Enteritidis, and Virchow were 0.72, 0.52, and 0.66, respectively. Within these serotypes the most common RAPD types were differentiated into phage types and vice versa; combining the types identified by the two procedures (RAPD typing and phage typing) resulted in further discrimination (DI, 0.96, 0.74, and 0.87, respectively). The efficiency, rapidity, and flexibility of the RAPD typing method support the conclusion that it can be used as a tool for identifying Salmonella organisms and as a typing method that is complementary to serotyping and phage typing methods.

THE EFFECTS OF AN EXPERIMENTAL INJECTION OF METHOXYCHLOR ON AQUATIC INVERTEBRATES: ACCUMULATION, STANDING CROP, AND DRIFT

1979 ◽  
Vol 111 (1) ◽  
pp. 73-89 ◽  
Author(s):  
J. F. Flannagan ◽  
B. E. Townsend ◽  
B. G. E. de March ◽  
M. K. Friesen ◽  
S. L. Leonhard
Keyword(s):  
Standing Crop ◽  
Close Agreement ◽  
Aquatic Invertebrates ◽  
Sampling Methods ◽  
Natural Populations ◽  
Environmental Damage ◽  
Percentage Reduction ◽  
Athabasca River ◽  
Time Required ◽  
Ambient Levels

AbstractA single 0.3 ppm injection of methoxychlor into the Athabasca River, Alberta on 4 June 1974 for 15 min caused catastrophic drift for a distance of over 400 km, and a subsequent large decrease in the drifting population. This decrease, when expressed as a percentage reduction from pretreatment drift, is in close agreement with percentage reduction of standing crop recorded by other sampling methods. The time required for the pesticide to affect different species varied considerably but was not related to the mode of feeding. Methoxychlor residues above ambient levels in water were recorded in all the invertebrate populations sampled. Caged animals had significantly different residues than the natural populations. The use of caged animals as indicators of environmental damage is therefore questioned.

scholarly journals Consequences of Long-term Exposure to Increased Salinity on the Amphibian Skin Bacterium Erwinia Toletana

2021 ◽  
Author(s):  
Antonieta Gabriel ◽  
Sara Costa ◽  
Isabel Henriques ◽  
Isabel Lopes
Keyword(s):  
Osmotic Stress ◽  
Recovery Period ◽  
Natural Populations ◽  
Amphibian Skin ◽  
Typing Method ◽  
Environmental Perturbations ◽  
Molecular Typing Method ◽  
Pelophylax Perezi ◽  
Skin Bacterium

Abstract Amphibian’s skin bacterial community may help them to cope with several types of environmental perturbations, including osmotic stress caused by increased salinity. This work aimed at assessing if an amphibian skin bacterium could increase its tolerance to NaCl after a long-term exposure to this salt. A strain of Erwinia toletana, isolated from the skin of Pelophylax perezi, was exposed to two salinity scenarios (of 18g/L of NaCl): (i) long-term exposure (for 46 days; Et-NaCl) and (ii) long-term exposure followed by a recovery period, (exposure for 30 days to NaCl and then to LB medium for 16 days; Et-R). After exposure, the sensitivity of E. toletana clonal populations to NaCl was assessed by testing 6 NaCl concentrations (LB medium spiked with NaCl) plus a control (LB medium). Genotypic alterations were assessed by PCR-based molecular typing method (BOX-PCR). Results shown that tolerance of E. toletana to NaCl slightly increased after the long-term exposure, EC50 for growth were: 22.5g/L (8.64-36.4) for Et-LB; 30.3g/L (23.2-37.4) for Et-NaCl, and 26.1g/L (19.3-32.9) for Et-R. Differences in metabolic activity were observed between Et-LB and Et-R and Et-NaCl and Et-R suggesting the use of different substrates by this bacterium when exposed to salinized environments. NaCl-induced genotypic alterations were not detected. This work suggests that E. toletana exposed to low levels of salinity, activate different metabolic pathways to cope with osmotic stress. Which may be further explored to be used in bioaugmentation procedures in natural populations of amphibians exposed to salinization.

Molecular Epidemiology in the Care of Patients

1999 ◽  
Vol 123 (11) ◽  
pp. 1007-1010
Author(s):  
Michael A. Pfaller
Keyword(s):  
Molecular Typing ◽  
Restriction Endonuclease Analysis ◽  
Microbial Pathogens ◽  
Chromosomal Dna ◽  
Typing Method ◽  
Epidemiologic Surveillance ◽  
Term Evaluation ◽  
Typing Methods ◽  
Plasmid Profiling

Abstract Several different epidemiologic typing methods have been applied in studies of microbial pathogens. These methods include the more traditional nonmolecular approaches as well as the more sophisticated molecular typing methods. Application of traditional epidemiologic typing methods, such as antibiogram, serotyping, biotyping, and phage typing, have occasionally been useful in describing the epidemiology of infectious diseases. However, these methods have generally been considered to be too variable, labor intensive, and slow to be of practical value in epidemiologic investigations. In response to these limitations, several techniques have been adopted from the molecular biology field for use as epidemiologic typing methods and have been applied in studies of bacteria, fungi, viruses, and protozoa. The most widely used molecular typing methods are the DNA-based methods, such as plasmid profiling, restriction endonuclease analysis of plasmid and genomic DNA, Southern hybridization analysis using specific DNA probes, and chromosomal DNA profiling using either pulsed-field gel electrophoresis or polymerase chain reaction–based methods. The various molecular typing methods may be applied to the investigation of outbreaks of infections or may be used in the context of epidemiologic surveillance. For outbreak investigation, typing methods are used to compare isolates from a suspected outbreak to delineate clonally related and unrelated strains with the goal of short-term control of transmission. In the context of epidemiologic surveillance, molecular typing methods may be used to monitor geographic spread and prevalence shifts of epidemic and endemic clones with the goal of long-term evaluation of preventive strategies or for the detection and monitoring of emerging and reemerging infections. The specific typing method selected may vary with the task at hand; however, the typing studies must always be used to supplement, rather than replace, careful epidemiologic investigation.

Micro-broth dilution method with air-dried microplate for determining MICs of clarithromycin and amoxycillin for Helicobacter pylori isolates

2004 ◽  
Vol 53 (5) ◽  
pp. 403-406 ◽  
Author(s):  
Intetsu Kobayashi ◽  
Hiroe Muraoka ◽  
Takeshi Saika ◽  
Minoru Nishida ◽  
Toshio Fujioka ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Close Agreement ◽  
Reliable Method ◽  
Agar Plate ◽  
Dilution Method ◽  
Air Drying ◽  
H Pylori ◽  
Broth Dilution

MICs of clarithromycin and amoxycillin for 253 isolates of Helicobacter pylori were measured by an air-dried microplate method and compared with the results obtained by the agar plate dilution method. The air-dried microplate method is performed by coating each well of a 96-well microplate with the test antibiotic and air-drying it. There were no marked differences between the air-dried microplate method and agar plate dilution methods in the MIC50 and MIC90 values or MIC ranges of clarithromycin obtained for the 253 isolates of H. pylori. More specifically, the MICs of clarithromycin for 114 (45.1 %) of the 253 isolates were the same by the air-dried microplate method as the agar plate dilution method, and the differences in the MICs of clarithromycin for a further 114 isolates (45.1 %) varied within one twofold dilution. The MICs of amoxycillin by the former method were in close agreement with the MICs obtained by the latter method: MICs of amoxycillin for 199 (78.7 %) of the 253 isolates were the same by both methods, and the differences in the MICs of amoxycillin for 42 isolates (16.6 %) varied within one twofold dilution. These results indicate that the air-dried microplate method is a useful method for determination of MICs, because the results obtained were in close agreement with those obtained by the standard agar plate dilution method. The air-dried microplate method is, therefore, a convenient and reliable method for determining the MICs of clarithromycin and amoxycillin for H. pylori isolates.

scholarly journals Comparison of multilocus enzyme electrophoresis (MEE), ribotyping, restriction enzyme analysis (REA) and phage typing for typing ofListeria monocytogenes

1993 ◽  
Vol 111 (1) ◽  
pp. 71-79 ◽  
Author(s):  
B. Nørrung ◽  
P. Gerner-Smith
Keyword(s):  
Listeria Monocytogenes ◽  
Molecular Typing ◽  
Phage Typing ◽  
Enzyme Analysis ◽  
Restriction Enzyme Analysis ◽  
Enzyme Electrophoresis ◽  
Typing Method ◽  
Multilocus Enzyme Electrophoresis ◽  
Serotype 1 ◽  
Typing Methods

SummaryThe discriminatory power of four methods for typing ofListeria monocytogeneswas compared. The four methods were multilocus enzyme electrophoresis (MEE), ribotyping, restriction enzyme analysis (REA), and a newly developed Danish phage typing system. Ninety-nine human clinical, food and slaughterhouse isolates ofListeria monocytogeneswere typed by each method. The most discriminatory single typing method was phage typing with an overall discriminatory index (DI) of 0·88 followed by REA, MEE and ribotyping with DI-values at 0·87, 0·83 and 0·79 respectively. Considering strains from each of the two predominant O-serotypes alone, serotype 1 was best discriminated by the molecular typing methods, in particular REA, which showed a DI of 0·92. The serotype 4 strains were best discriminated by phage typing (DI = 0·78). If two or more typing methods were combined, the combination of REA and MEE were found to be the most discriminatory combination. The DI values were 0·96, 0·74 and 0·90 for serotype 1, 4, and both combined, respectively. Phage typing is a rapid and inexpensive typing method but not as reproducible as the molecular typing methods. It is the most suitable method for mass screening. In situations where results are required to be highly reliable, i.e. when studying the relationships between only a few strains, a single or a combination of molecular typing methods should be used, preferable MEE and REA.

scholarly journals Staphylococcal Cassette Chromosome mec (SCCmec) Classification and Typing Methods: an Overview

2011 ◽  
Vol 60 (2) ◽  
pp. 95-103 ◽  
Author(s):  
AGATA TURLEJ ◽  
WALERIA HRYNIEWICZ ◽  
JOANNA EMPEL
Keyword(s):  
Current Knowledge ◽  
Sccmec Type ◽  
Spa Typing ◽  
Typing Method ◽  
Hospital Acquired Infections ◽  
Advantages And Disadvantages ◽  
Type Assignment ◽  
Typing Methods ◽  
New Type ◽  
Hospital Acquired

Meticillin-resistant Staphylococcus aureus (MRSA) is one of the main causes of hospital-acquired infections, but since late 1990s also the community-acquired. For better understanding of the S.aureus epidemiology there is an urgent need for creation of new typing method for SCCmec element. The molecular typing of MRSA for epidemiological purposes is investigated by pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), spa typing and the SCCmec type assignment. In last few years not only new type of SCCmec (VI to XI) have been identified, but also additional subtypes (i.e. IVg-j) and different variants of already existed one (i.e. 5C2&5 and 2B2&5) were discovered. The aim of this review is to briefly summarize current knowledge about SCCmec classification and to discuss advantages and disadvantages of selected SCCmec typing methods.

scholarly journals CoxBase: an online platform for epidemiological surveillance, visualization, analysis and typing of Coxiella burnetii genomic sequence

2020 ◽  
Author(s):  
Akinyemi. M. Fasemore ◽  
Andrea Helbich ◽  
Mathias. C. Walter ◽  
Thomas Dandekar ◽  
Gilles Vergnaud ◽  
...  
Keyword(s):  
Coxiella Burnetii ◽  
In Silico ◽  
Genomic Sequence ◽  
Control Measure ◽  
Small Ruminants ◽  
Epidemiological Surveillance ◽  
Typing Method ◽  
Country Level ◽  
Central Platform ◽  
Typing Methods

ABSTRACTQ (query) fever is an infectious zoonotic disease, caused by the Gram-negative bacteria Coxiella burnetii, that sometimes is transmitted to humans from small ruminants like sheep, goat and cattle. Although the disease has been studied since decades, it still represents a threat due to sporadic outbreaks across farms in Europe. The reason for this has been linked to the interaction of several dynamic factors including reservoir type and vector diversity. One important control measure we have identified is a central platform for Coxiella typing data management. This is particularly important in the case of an outbreak where the nature of the pathogen and type would need to be rapidly identified and compared to existing isolates as well as further documented and made available for researcher to aid future investigations. The existing platforms are focused on MLVA (multiple locus VNTR analysis) genotyping. We have designed and implemented an online, open, web-based platform called CoxBase (https://coxbase.q-gaps.de), that is capable of in silico genotyping of completely or minimally assembled Coxiella sequences using five different typing methods, included with a database that holds genotyping information of more than 400 Coxiella isolates with their metadata such as host type, source and year of isolation together with further metadata information. Also, it includes a query and submission interface for interrogating existing isolates and depositing new isolates. Attractive visualization features include maps showing the geographical source of the isolates and plots that can be used to summarize isolates metadata on a country level. We tested our in silico typing method on 50 Coxiella genomes downloaded from the RefSeq database and we could type almost all the genomes except for cases where the sequences are poorly assembled. We identified new spacer sequences using our MST in silico typing methods, and could categorize adaA gene phenotypes for all 50 genomes as well as their plasmid types.

scholarly journals A comparison of typing methods forSerratia marcescens

1977 ◽  
Vol 79 (1) ◽  
pp. 89-102 ◽  
Author(s):  
B. Anderhub ◽  
T. L. Pitt ◽  
Y. J. Erdman ◽  
W. R. Willcox
Keyword(s):  
Production Method ◽  
Induction Method ◽  
Typing Method ◽  
Simple Method ◽  
Clear Cut ◽  
Typing Methods ◽  
The Cross ◽  
Inhibition Experiment ◽  
Acceptable Reliability ◽  
Producer Strains

SUMMARYA simple method for the bacteriocine typing ofSerratia marcescenswithout the use of induction was sought. The results of a mutual inhibition experiment with 89 unrelated cultures indicated that a bacteriocine-susceptibility method would give more discrimination between strains than would a bacteriocine-production method. A cross-streaking technique for bacteriocine-susceptibility typing without previous induction was developed, and its performance was compared with that of another susceptibility-typing method in which cell-free lysates of the producer strains were obtained by induction with mitomycin C.Replicate typing of the same collection of cultures by both methods indicated that small variations in pattern were common and that larger variations occurred occasionally. Differences in pattern of less than two strong reactions in the mito-mycin-C induction method, and of less than three strong reactions in the cross-streaking method, should therefore not be taken as evidence that strains can be distinguished.Sets of cultures ofSer. marcescens, 178 in total, from a number of supposed incidents of infection in hospitals, were used to evaluate the two bacteriocine-typing methods; all of the cultures were also O serogrouped. Comparison of the typing patterns of members of the same O serogroup from clear-cut incidents of infection confirmed that results of acceptable reliability could be obtained by either bacteriocine-typing method by the application of the appropriate 'difference' rule. When so interpreted, the cross-streaking method appeared to be slightly the more discriminatory.The greatest discrimination between strains was obtained by the use of a 'hierarchical' typing system in which the strains were first O serogrouped, and the cross-streaking method of bacteriocine typing was then used to make subdivisions within O serogroups.

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