Fingerprinting 2 software

Manufactured by Bio-Rad

Sourced in United States, France

Fingerprinting II software is a tool used for analyzing DNA fingerprints. It provides a platform for storing, managing, and comparing DNA profiles. The software enables users to perform statistical analysis on DNA data.

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Lab products found in correlation

Xbai, by Takara Bio (3 mentions) Chef mapper, by Bio-Rad (3 mentions) N0340s lambda ladder pfg marker, by New England Biolabs (2 mentions) Chef dr 2 system, by Bio-Rad (1 mentions) Maldi biotyper 2, by Bruker (1 mentions) Lambda ladder pfg marker, by New England Biolabs (1 mentions) Quantity one software, by Bio-Rad (1 mentions) Sybr gold stain, by Thermo Fisher Scientific (1 mentions) Pulsed field certified agarose, by Bio-Rad (1 mentions) Xbai endonuclease, by New England Biolabs (1 mentions) Chef mapper system, by Bio-Rad (1 mentions) Chef dr 2, by Bio-Rad (1 mentions) Chef drii apparatus, by Bio-Rad (1 mentions)

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Fingerprinting II Informatix Software Fingerprinting II

10 protocols using fingerprinting 2 software

Profiling and Typing Acinetobacter baumannii

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The MSP profile showing the highest score was selected for each isolate and was included to construct the dendrogram using the statistical toolbox in MATLAB 7.1 integrated in the MALDI Biotyper 2.0 software (Bruker Daltonics). Based on the principle that identification score reflects the agreement of the spectra with the standard A. baumannii database entry, the MSP profile showing the highest score could mean that the specific spectra represents the most typical aspects of a certain strain from the database. This selection of the highest score marking spectra was necessary, especially when highly similar strains were studied, because several mass spectral features related to limited reproducibility of the method might eclipse mass spectral differences between the strains. Test strain clonality was determined with cut-off values at a distance of 250 [6 (link)].
For PFGE analysis of the 32 isolates, SmaI-digested genomic DNA was prepared according to the manufacturer's instructions (Bio-Rad, Hercules, CA, USA). Fragments were separated for 20 h at 6.0 V/cm at 11°C using a CHEF-DR II System (Bio-Rad) with initial and final pulse times of 0.5 s and 30 s, respectively [14 (link)]. The pattern was analyzed using the Fingerprinting II software (Bio-Rad). The cut-off value of 75 was applied for grouping as it was used previously [15 (link), 16 (link)].

Rim J.H., Lee Y., Hong S.K., Park Y., Kim M., D'Souza R., Park E.S., Yong D, & Lee K. (2015). Insufficient Discriminatory Power of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry Dendrograms to Determine the Clonality of Multi-Drug-Resistant Acinetobacter baumannii Isolates from an Intensive Care Unit. BioMed Research International, 2015, 535027.

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Genomic DNA Fingerprinting of Enterobacteriaceae

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K. pneumoniae, C. freundii complex, and M. morganii genomic DNAs, in gel-embedded form, were digested with XbaI (TaKaRa Bio, Shiga, Japan). Pulsed-field gel electrophoresis (PFGE) was performed using CHEF Mapper (Bio-Rad, Hercules, CA, USA) in 1× Tris-borate-EDTA (TBE) buffer, along with Lambda Ladder PFG marker (New England Biolabs, Hertfordshire, United Kingdom). Fingerprinting II software (Bio-Rad) was used to analyze the electrophoretic patterns, and the analysis parameters were as follows: the Dice coefficient, the unweighted pair group method with averages, 1% position tolerance, and 1% optimization.

Sugita K., Aoki K., Komori K., Nagasawa T., Ishii Y., Iwata S, & Tateda K. (2021). Molecular Analysis of blaKPC-2-Harboring Plasmids: Tn4401a Interplasmid Transposition and Tn4401a-Carrying ColRNAI Plasmid Mobilization from Klebsiella pneumoniae to Citrobacter europaeus and Morganella morganii in a Single Patient. mSphere, 6(6), e00850-21.

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Denaturing Gradient Gel Electrophoresis Analysis

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All DGGE analyses were performed using the INGENYphorU-2x2 system (INGENY International, Amundsenweg, The Netherlands). Amplicons were analyzed on 8% polyacrylamide (40% acrylamide-bis, 37.5∶1) gel with a 40% to 65% denaturing gradient of urea and formamide increasing in the direction of electrophoresis. The gel was run with a constant voltage of 80 V at 60°C for 18 h in 1× Tris-acetate buffer (pH 8.0).
The Fingerprinting II software([Bio-Rad, Hercules CA, USA) was used to compare DGGE profiles using the Pearson’s similarity coefficient for comparison and the UPGMA algorithm for the dendrogram construction. The Quantity One software([version 4.6.0; Bio-Rad, Hercules CA, USA) was used for the identification and quantification of bands.

Bruzzese E., Callegari M.L., Raia V., Viscovo S., Scotto R., Ferrari S., Morelli L., Buccigrossi V., Lo Vecchio A., Ruberto E, & Guarino A. (2014). Disrupted Intestinal Microbiota and Intestinal Inflammation in Children with Cystic Fibrosis and Its Restoration with Lactobacillus GG: A Randomised Clinical Trial. PLoS ONE, 9(2), e87796.

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PFGE-Based Bacterial Strain Typing

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In accordance with the standardized PulseNet protocol maintained at the Center for Disease Control and Prevention, we performed pulsed-field gel electrophoresis (Hunter et al., 2005 (link)). Strains grown on TSA medium were collected by a cotton swab and then resuspended in 1 ml of Tris-EDTA buffer (10 mM Tris–HCl, 1 mM EDTA, pH 8.0) to an OD_600nm of 0.5–0.7. After lysozyme and proteinase K treatments, plugs were incubated in EC lysis buffer (6 mM Tris–HCl, 1 M NaCl, 100 mM EDTA, 0.5% Brij-58, 0.2% sodium deoxycholate, 0.5% sodium lauroly sarcosine). The plugs were digested with SmaI (Takara), and the genomic DNA fragments were separated in a 1% Seakem gold agarose gel using a CHEF Mapper (Bio-Rad, Hercules, CA, USA) system. Gels were stained with SYBR^® Gold Stain (Invitrogen, USA). The cellular DNA from Salmonella serotype Braenerup H9812 was treated with XbaI (Takara) and that DNA fragments were used as a standard for normalization (Hunter et al., 2005 (link)). Using the Fingerprinting II software (Bio-Rad), PFGE band patterns were analyzed, and a dendrogram was clustered and analyzed using the un-weighted pair group method of average linkage (UPGMA).

Lee D.H., Kim J.B., Lim J.A., Han S.W, & Heu S. (2014). Genetic Diversity of Pectobacterium carotovorum subsp. brasiliensis Isolated in Korea. The Plant Pathology Journal, 30(2), 117-124.

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PFGE Analysis of ESBL-Ec Isolates

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To examine the clonal relationship among the ESBL-Ec isolates, PFGE analysis was carried out according to the Pulse Net USA protocol (https://www.cdc.gov/pulsenet/pdf/ecoli-shigella-salmonella-pfge-protocol-508c.pdf) with slight modifications.
Briefly, genomic DNA of the isolates was digested with 30 U of XbaI (TaKaRa Bio Inc., Kusatsu, Japan) at 37°C for 2 hr. XbaI-digested Salmonella enterica serotype
Braenderup H9812 was used as a molecular size marker. The digested DNA was electrophoresed on 1.0% pulsed-field certified agarose (Bio-Rad Laboratories Inc., Hercules, CA, U.S.A.) in 0.5X TBE (45 mM Tris, 45 mM boric
acid, 1 mM EDTA) buffer at 6 V/cm², with a switch time of 6.76–35.38 sec for 27 hr using a CHEF Mapper (Bio-Rad Laboratories Inc.). The gel was stained with ethidium bromide and de-stained with distilled
water. The DNA fingerprint patterns were photographed with UV gel Doc (Bio-Rad Laboratories, Inc.) and analyzed by Fingerprinting II software (Bio-Rad Laboratories Inc.). Dendrogram analysis was performed using the
unweighted-pair group method with arithmetic mean (UPGMA) analysis and the band-based (Dice correlation coefﬁcient) option.

NAHAR A., AWASTHI S.P., HATANAKA N., OKUNO K., HOANG P.H., HASSAN J., HINENOYA A, & YAMASAKI S. (2018). Prevalence and characteristics of extended-spectrum β-lactamase-producing Escherichia coli in domestic and imported chicken meats in Japan. The Journal of Veterinary Medical Science, 80(3), 510-517.

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Pulsed-Field Gel Electrophoresis of E. coli O157

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Representative O157 isolates were subjected to PFGE with XbaI endonuclease (New England BioLabs, Ipswich, MA, USA) using the CHEF Mapper system (Bio-Rad Laboratories, Hercules, CA, USA) as described previously [8 (link)]. The gel images were obtained using ethidium bromide stain. The electrophoretic patterns from PFGE were compared based on band position using FingerPrinting II software (Bio-Rad Laboratories, Hercules, CA, USA) and derived using the Dice coefficient with a maximum position tolerance of 1%. The strains were clustered using the unweighted pair group (UPGMA) method with arithmetic averages according to the manufacturer's instructions.

Asakura H., Masuda K., Yamamoto S, & Igimi S. (2014). Molecular Approach for Tracing Dissemination Routes of Shiga Toxin-Producing Escherichia coli O157 in Bovine Offal at Slaughter. BioMed Research International, 2014, 739139.

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Pulsed-Field Gel Electrophoresis for Bacterial Genotyping

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To determine the genetic relatedness of the isolates, pulsed-field gel electrophoresis (PFGE) was used, as described by Benson et al. [38 (link)]. The complete bacterial genome was embedded in agarose plugs and lysed in several steps (with lysozyme, mutanolysin and proteinase K) to purify DNA. For the digestion, Sma I restriction enzyme was used (3 h, 25 °C). The digested samples were run in a 1% agarose gel along with N0340S Lambda Ladder PFG Marker (New England Biolabs, Hitchin, Hertfordshire, UK), in a Bio-Rad CHEF-DR® II PFGE machine, for 21 h at 14 °C, with the following pulse times: block 1, 5 s/15 s for 10 h, and block 2, 15 s/60 s for 11 h. After the gel image was captured, dendrograms were created by the Fingerprinting II software (Bio-Rad, Marnes-la-Coquette, France) and the PFGE patterns were analysed according to the criteria of van Belkum et al. [39 (link)].

Kardos S., Tóthpál A., Laub K., Kristóf K., Ostorházi E., Rozgonyi F, & Dobay O. (2019). High prevalence of group B streptococcus ST17 hypervirulent clone among non-pregnant patients from a Hungarian venereology clinic. BMC Infectious Diseases, 19, 1009.

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Genomic DNA Isolation and Fingerprinting

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Genomic DNA was isolated by the modification of the salting-out procedure (MSOP) [48 (link),49 (link)]. Genomic fingerprints were obtained by RAPD using the M13 primer as described previously (Supplementary Table S1) [49 (link)]. Genomic fingerprints were clustered using the Fingerprinting II software (Bio-Rad) applying Pearson product moment correlation coefficient, and the corresponding dendrogram was constructed using the unweighted-pair-group method with arithmetic averages (UPGMA) [50 (link)]. To assess the reproducibility of RAPD profiles, each PCR was performed in triplicate.

Montalbán-López M., Cebrián R., Galera R., Mingorance L., Martín-Platero A.M., Valdivia E., Martínez-Bueno M, & Maqueda M. (2020). Synergy of the Bacteriocin AS-48 and Antibiotics against Uropathogenic Enterococci. Antibiotics, 9(9), 567.

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Genetic Relatedness Analysis by PFGE

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To determine the genetic relatedness of the isolates, pulsed-field gel electrophoresis (PFGE) was used as described earlier [14] . The complete bacterial genome was embedded in agarose plugs and lysed in several steps to purify DNA. For the digestion, Sma I restriction enzyme was used (3 h, 25 °C). The digested samples were run in a 1% agarose gel along with N0340S Lambda Ladder PFG Marker (New England Biolabs, Hitchin, Hertfordshire, UK), in a Bio-Rad CHEF-DR ® II PFGE machine, for 21 h at 14 °C, with the following pulse times: block one -5 s/15 s for 10 h, and block two -15 s/60 s for 11 h. After the gel image was captured, the PFGE patterns were analyzed and the dendrograms were created by the Fingerprinting II software (Bio-Rad).

Laub K., Tóthpál A., Kardos S, & Dobay O. (2017). Epidemiology and antibiotic sensitivity of Staphylococcus aureus nasal carriage in children in Hungary. Acta microbiologica et immunologica Hungarica, 64(1).

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Genomic Fingerprinting of A. baumannii

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A. baumannii DNA was digested with ApaI (TaKaRa, Dalian, Liaoning Province, China) as a restriction enzyme. DNA fragments were separated on 1% w/v agarose gels in 0.5Â Tris/borate/ ethylenediaminetetraacetic acid (TBE) buffer at 14 8C using a CHEF DRII apparatus (Bio-Rad) with 6 V/cm, pulsed from 3 to 20 s for 21 h; gels were stained with Gel Red. The Dice coefficient was used to calculate similarities, and the unweighted pair group method using average linkages (UPGMA) was used for cluster analysis with fingerprinting II software (Bio-Rad, Marne La Coquette, France). Isolates were considered to belong to the same PFGE clone if their Dice similarity index was !80%.

Al Atrouni A., Hamze M., Jisr T., Lemarié C., Eveillard M., Joly-Guillou M.L, & Kempf M. (2016). Wide spread of OXA-23-producing carbapenem-resistant Acinetobacter baumannii belonging to clonal complex II in different hospitals in Lebanon. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 52.

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