PulseNet international: the missing link between PFGE and WGS
Abstract Introduction DNA-based surveillance of bacterial diseases has been using pulsed field gel electrophoresis (PFGE) since 1996. Currently, the international surveillance network (PulseNet international) is turning toward whole genome sequencing (WGS). ATCGs of WGS are compared using several se...
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13.03.2021
Cold Spring Harbor Laboratory |
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| Abstract | Abstract Introduction DNA-based surveillance of bacterial diseases has been using pulsed field gel electrophoresis (PFGE) since 1996. Currently, the international surveillance network (PulseNet international) is turning toward whole genome sequencing (WGS). ATCGs of WGS are compared using several sequence alignment methods. While patterns of horizontal lines of PFGE profiles are being compared using relative positioning of bands within a range of tolerance. A recently suggested image analysis algorithm and a deployed database (geltowgs.uofk.edu) collectively invented a promising method for comparing PFGE to in-silico obtained digestion models (DMs) derived from WGS. The database requires a parameter that determines PFGE resolution. Here, the author suggests a new method for calculating this factor. Epidemiological and molecular conclusions returned by the database are evaluated. Methodology two PFGE profiles representing XbaI digests of E. coli and Salmonella enterica analyzed by the suggested image analysis algorithm were submitted to the database after calculating resolution of PFGE using Dice percentage of difference between the closest PFGE bands in length. E. coli and Salmonella enterica test subjects were compared to 489 and 401 DMs respectively. The three data sets returned were analyzed. Results and conclusions according to modified PFGE evaluation criteria; a single DM is possibly related to E. coli test subject. It belonged to the same serovar. No epidemiologically related DM was shown for S. enterica test subject. Conclusions mentioned earlier could never be made ignoring co-migration. Standardization of both; suggested image analysis and database algorithms will deepen our understanding of bacterial epidemiology by means of possible qualitative approach built upon identification of fragment sequences and their locations within chromosomes. Competing Interest Statement The authors have declared no competing interest. Footnotes * correcting some typos, rearranging some sentences and replacing some words. |
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| AbstractList | Abstract Introduction DNA-based surveillance of bacterial diseases has been using pulsed field gel electrophoresis (PFGE) since 1996. Currently, the international surveillance network (PulseNet international) is turning toward whole genome sequencing (WGS). ATCGs of WGS are compared using several sequence alignment methods. While patterns of horizontal lines of PFGE profiles are being compared using relative positioning of bands within a range of tolerance. A recently suggested image analysis algorithm and a deployed database (geltowgs.uofk.edu) collectively invented a promising method for comparing PFGE to in-silico obtained digestion models (DMs) derived from WGS. The database requires a parameter that determines PFGE resolution. Here, the author suggests a new method for calculating this factor. Epidemiological and molecular conclusions returned by the database are evaluated. Methodology two PFGE profiles representing XbaI digests of E. coli and Salmonella enterica analyzed by the suggested image analysis algorithm were submitted to the database after calculating resolution of PFGE using Dice percentage of difference between the closest PFGE bands in length. E. coli and Salmonella enterica test subjects were compared to 489 and 401 DMs respectively. The three data sets returned were analyzed. Results and conclusions according to modified PFGE evaluation criteria; a single DM is possibly related to E. coli test subject. It belonged to the same serovar. No epidemiologically related DM was shown for S. enterica test subject. Conclusions mentioned earlier could never be made ignoring co-migration. Standardization of both; suggested image analysis and database algorithms will deepen our understanding of bacterial epidemiology by means of possible qualitative approach built upon identification of fragment sequences and their locations within chromosomes. Competing Interest Statement The authors have declared no competing interest. Footnotes * correcting some typos, rearranging some sentences and replacing some words. DNA-based surveillance of bacterial diseases has been using pulsed field gel electrophoresis (PFGE) since 1996. Currently, the international surveillance network (PulseNet international) is turning toward whole genome sequencing (WGS). ATCGs of WGS are compared using several sequence alignment methods. While patterns of horizontal lines of PFGE profiles are being compared using relative positioning of bands within a range of tolerance. A recently suggested image analysis algorithm and a deployed database (geltowgs.uofk.edu) collectively invented a promising method for comparing PFGE to in-silico obtained digestion models (DMs) derived from WGS. The database requires a parameter that determines PFGE resolution. Here, the author suggests a new method for calculating this factor. Epidemiological and molecular conclusions returned by the database are evaluated. two PFGE profiles representing XbaI digests of E. coli and Salmonella enterica analyzed by the suggested image analysis algorithm were submitted to the database after calculating resolution of PFGE using Dice percentage of difference between the closest PFGE bands in length. E. coli and Salmonella enterica test subjects were compared to 489 and 401 DMs respectively. The three data sets returned were analyzed. according to modified PFGE evaluation criteria; a single DM is possibly related to E. coli test subject. It belonged to the same serovar. No epidemiologically related DM was shown for S. enterica test subject. Conclusions mentioned earlier could never be made ignoring co-migration. Standardization of both; suggested image analysis and database algorithms will deepen our understanding of bacterial epidemiology by means of possible qualitative approach built upon identification of fragment sequences and their locations within chromosomes. |
| Author | Adam, Ibrahim-Elkhalil M |
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| DOI | 10.1101/2021.03.08.434411 |
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| References_xml | – year: 2006 ident: 2021.03.08.434411v2.3 article-title: Building PulseNet International: An Interconnected System of Laboratory Networks to Facilitate Timely Public Health Recognition and Response to Foodborne Disease Outbreaks and Emerging Foodborne Diseases publication-title: Foodborne Pathog Dis – volume: 3 start-page: 52 issue: 2 year: 2020 end-page: 67 ident: 2021.03.08.434411v2.11 article-title: Novel algorithms for PFGE bacterial typing: Number of co-migrated DNA fragments, linking PFGE to WGS results and computer simulations for evaluation of PulseNet international typing protocols publication-title: J Appl Microbiol Res – ident: 2021.03.08.434411v2.20 publication-title: NebCutter|New England BioLabs Inc – volume: 43 start-page: 1045 issue: 3 year: 2005 end-page: 50 ident: 2021.03.08.434411v2.5 article-title: Establishment of a universal size standard strain for use with the pulsenet standardized pulsed-field gel electrophoresis protocols: Converting the national databases to the new size standard publication-title: J Clin Microbiol – volume: 9 start-page: 1 issue: 5 year: 2014 end-page: 7 ident: 2021.03.08.434411v2.6 article-title: Plasmid profile and pulsed-field gel electrophoresis analysis of Salmonella enterica isolates from humans in Turkey publication-title: PLoS One – volume: 22 start-page: 1 issue: 23 year: 2017 end-page: 12 ident: 2021.03.08.434411v2.4 article-title: PulseNet International : Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance publication-title: Euro Surveill – volume: 10 start-page: 866 issue: 7 year: 2010 end-page: 75 ident: 2021.03.08.434411v2.13 article-title: Pulsed field gel electrophoresis: A review of application and interpretation in the molecular epidemiology of infectious disease publication-title: Infect Genet Evol [Internet] – volume: 9 issue: 6 year: 2018 ident: 2021.03.08.434411v2.8 article-title: Salmonella enterica phylogeny based on whole-genome sequencing reveals two new clades and novel patterns of horizontally acquired genetic elements publication-title: MBio – volume: 13 start-page: 1 issue: SUPPL. 3 year: 2007 end-page: 46 ident: 2021.03.08.434411v2.19 article-title: Guidelines for the validation and application of typing methods for use in bacterial epidemiology publication-title: Clin Microbiol Infect – volume: 15 start-page: 5985 issue: 15 year: 1987 end-page: 6005 ident: 2021.03.08.434411v2.1 article-title: Restriction endonucleases for pulsed field mapping of bacterial genomes publication-title: Nucleic Acids Res [Internet] – volume: 16 start-page: 457 issue: 7 year: 2019 end-page: 62 ident: 2021.03.08.434411v2.2 article-title: An Overview of PulseNet USA Databases publication-title: Foodborne Pathog Dis – volume: 112 start-page: E3574 issue: 27 year: 2015 end-page: 81 ident: 2021.03.08.434411v2.7 article-title: Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health publication-title: Proc Natl Acad Sci U S A – volume: 36 start-page: 1653 issue: 6 year: 1998 end-page: 9 ident: 2021.03.08.434411v2.12 article-title: Assessment of resolution and intercenter reproducibility of results of genotyping Staphylococcus aureus by pulsed-field gel electrophoresis of SmaI macrorestriction fragments: A multicenter study publication-title: J Clin Microbiol – start-page: e8 year: 2014 end-page: e8 ident: 2021.03.08.434411v2.17 article-title: Molecular Microbiology: Diagnostic Principles and Practice, 2 nd edition publication-title: In: Laboratory Medicine [Internet] – volume: 46 start-page: 2766 issue: 8 year: 2008 end-page: 73 ident: 2021.03.08.434411v2.15 article-title: Evaluation and validation of a PulseNet standardized pulsed-field gel electrophoresis protocol for subtyping Vibrio parahaemolyticus: An International Multicenter Collaborative study publication-title: J Clin Microbiol – start-page: 159 year: 2001 end-page: 76 ident: 2021.03.08.434411v2.10 article-title: Analysis of Microbial Genomic Macrorestriction Patterns by Pulsed-Field Gel Electrophoresis (PFGE) Typing publication-title: New Approaches Gener Anal Microb Typing Data – volume: 5 start-page: 21 issue: 1 year: 2003 end-page: 7 ident: 2021.03.08.434411v2.16 article-title: Method for optimizing pulsed-field gel electrophoresis banding pattern data publication-title: J Mol Diagnostics [Internet] – year: 2019 ident: 2021.03.08.434411v2.9 publication-title: PulseNet International: On the path to implementing whole genome sequencing for foodborne disease surveillance [Internet]. 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| Snippet | Abstract Introduction DNA-based surveillance of bacterial diseases has been using pulsed field gel electrophoresis (PFGE) since 1996. Currently, the... DNA-based surveillance of bacterial diseases has been using pulsed field gel electrophoresis (PFGE) since 1996. Currently, the international surveillance... |
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| SubjectTerms | Algorithms Chromosomes E coli Epidemiology Gel electrophoresis Genomes Image processing Microbiology Nucleotide sequence Salmonella Salmonella enterica Standardization Surveillance Whole genome sequencing |
| Title | PulseNet international: the missing link between PFGE and WGS |
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