A survey of tools for analysing DNA fingerprints

Heras, Jónathan; Domínguez, César; Mata, Eloy; Pascual, Vico; Lozano, Carmen; Torres, Carmén; Zarazaga, Myriam

doi:10.1093/bib/bbv016

Cited by 26 publications

(35 citation statements)

References 34 publications

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“…Pulsed-field gel electrophoresis (PFGE) of Xbal-digested genomic DNA samples of 15 selected CR-hvKp isolates was performed with a CHEF MAPPER XA apparatus (Bio-Rad, United States). PFGE patterns were analyzed using GelJ software 2.0v (Heras et al, 2015).…”

Section: Molecular Typing and Screening Of Antibiotic Resistance Genesmentioning

confidence: 99%

In vitro Activity of Apramycin Against Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae Isolates

Hao

Shi

et al. 2020

Front. Microbiol.

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Objective: The emergence of carbapenem-resistant and hypervirulent Klebsiella pneumoniae (CR-hvKp) strains poses a significant public threat, and effective antimicrobial therapy is urgently needed. Recent studies indicated that apramycin is a potent antibiotic with good activity against a range of multi-drug resistant pathogens. In this study, we evaluated the in vitro activity of apramycin against clinical CR-hvKp along with carbapenem-resistant non-hvKp (CR-non-hvKp) isolates.Methods: Broth microdilution method was used to evaluate the in vitro activities of apramycin, gentamicin, amikacin, imipenem, meropenem, doripenem, ertapenem and other comparator "last-resort" antimicrobial agents, including ceftazidime-avibactam, colistin and tigecycline, against eighty-four CR-hvKp and forty CR-non-hvKp isolates collected from three Chinese hospitals. Multilocus Sequence typing (MLST), molecular capsule typing (wzi sequencing) and antimicrobial resistance genes were examined by PCR and Sanger sequencing. Pulsed-field gel electrophoresis and next generation sequencing were conducted on selected isolates.Results: Among the 84 CR-hvKp isolates, 97.6, 100, 97.6, and 100% were resistant to imipenem, meropenem, doripenem and ertapenem, respectively. Apramycin demonstrated an MIC 50 /MIC 90 of 4/8 µg/mL against the CR-hvKp isolates. In contrast, the MIC 50 /MIC 90 for amikacin and gentamicin were >64/>64 µg/mL. All CR-hvKp isolates were susceptible to ceftazidime-avibactam, colistin and tigecycline with the MIC 50 /MIC 90 values of 0.5/1, 0.25/0.5, 1/1, respectively. For CR-non-hvKp, The MIC 50/90 values for apramycin, gentamicin and amikacin were 2/8, >64/>64, and >64/>64 µg/mL, respectively. There were no statistical significance in the resistance rates of antimicrobial agents between CR-hvKp and CR-non-hvKp groups (p > 0.05). Genetic analysis revealed that all CR-hvKp isolates harbored bla KPC-2 , and 94% (n = 79) belong to the ST11 high-risk clone. 93.6% (44/47) of amikacin or gentamicin resistant strains carried 16S rRNA methyltransferases gene rmtB.

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Section: Molecular Typing and Screening Of Antibiotic Resistance Genesmentioning

confidence: 99%

In vitro Activity of Apramycin Against Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae Isolates

Hao

Shi

et al. 2020

Front. Microbiol.

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“…Amplicons containing diverse microbial sequences are separated using electrophoresis in acrylamide gels, producing patterns of migrating DNA bands that are then photographed, digitized, and analyzed using commercial software such as GelCompar and Bionumerics, freeware such as GelClust, or a variety of other programs reviewed by Heras et al. (). With a few procedural modifications, community fingerprinting methods (except DGGE) can have their fluorescently tagged amplicons analyzed on DNA‐sequencing machines for a few dollars per sample, greatly improving the resolution, reproducibility, and quality of the data.…”

Section: Comparing Dna‐based Methods For Studying Plant Microbiomes (mentioning

confidence: 99%

Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant‐associated communities of bacteria and fungi

Johnston‐Monje

Mejía

2020

Appl Plant Sci

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High‐throughput sequencing technologies have revolutionized the study of plant‐associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant‐associated microbiomes using molecular fingerprinting methodologies, including single‐strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), amplicon length heterogeneity PCR (LH‐PCR), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP). We also present data juxtaposing results from TRFLP methods with those generated using Illumina sequencing in the comparison of rhizobacterial populations of Brazilian maize and fungal surveys in Canadian tomato roots. In both cases, the TRFLP approach yielded the desired results at a level of resolution comparable to that of the MiSeq method, but at a fraction of the cost. Community fingerprinting methods (especially TRFLP) remain relevant for the identification of dominant microbes in a population, the observation of shifts in plant microbiome community diversity, and for screening samples before their use in more sensitive and expensive approaches.

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“…GelScan, Phoretix 1D and Quantity are three commercial software which however they have the ability to make manual and automatic detection and generate the dendrogram, but the core problem of them is their high price, and the user must be exercised enough to be able to deal with them [9]. All available gel electrophoresis image analyzer tools [10] up to now are shown in Table 1 ordered by the last release of the gel image analyzer tool.…”

Section: Related Workmentioning

confidence: 99%

EGBIOIMAGE: A Software Tool for Gel Images Analysis and Hierarchical Clustering

2020

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This paper presents a novel software called EGBioImage that is implemented for analyzing gel Electrophoresis images, computing the molecular weights of the bands of the unknown size, detecting the types of the bands, grouping the bands according to their molecular weights and labeled each band with its group number in the gel image and generating the corresponding phylogenetic tree using the data extracted from the analyzed gel image. Students and Researchers working in molecular biology and genetics would benefit greatly from EGBioImage. This software is designed and developed under windows operating system using a C-sharp programming language. It uses Emgu CV platform to extract contours objects from an image that uses the green theorem to detect the bands in each detected lane. It uses polynomial regression to calculate the molecular weights of the bands of unknown size. It uses K-means clustering algorithm to cluster bands according to their molecular weights. It uses each of upgma algorithm and the matching bands amongst lanes and to construct the phylogenetic tree. EGBioImage provides a very friendly Graphical User Interface that guides the user from the step of uploading a gel image toward getting the molecular weights of the bands of unknown size and generating the Phylogenetic Tree. Moreover, EGBioImage provides the user with the ability of processing the gel image using a completely manual processing and automatic processing with the ability of manual correction of lanes and bands ''Semi-automatic process'' and it is more accurate than comparable software in some respects and the only software that divides the bands into groups and labeled them with numbers in the gel image based on their group by implementing k-means algorithm and these claims are supported with experiments. EGBioImage is suitable for students and researchers who do not have access to commercial software. INDEX TERMS Gel electrophoresis, image processing, phylogenetic tree, band matching, polynomial regression, UPGMA algorithm, k-means algorithm, software.

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A survey of tools for analysing DNA fingerprints

Cited by 26 publications

References 34 publications

In vitro Activity of Apramycin Against Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae Isolates

In vitro Activity of Apramycin Against Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae Isolates

Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant‐associated communities of bacteria and fungi

EGBIOIMAGE: A Software Tool for Gel Images Analysis and Hierarchical Clustering

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