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      chewBBACA: A complete suite for gene-by-gene schema creation and strain identification

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          Abstract

          Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers. The chewBBACA software uses Python 3.4 or higher and can run on a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. ChewBBACA is available at https://github.com/B-UMMI/chewBBACA.

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          Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms.

          M. C. J. Maiden, J. Bygraves, E Feil … (1998)
          Traditional and molecular typing schemes for the characterization of pathogenic microorganisms are poorly portable because they index variation that is difficult to compare among laboratories. To overcome these problems, we propose multilocus sequence typing (MLST), which exploits the unambiguous nature and electronic portability of nucleotide sequence data for the characterization of microorganisms. To evaluate MLST, we determined the sequences of approximately 470-bp fragments from 11 housekeeping genes in a reference set of 107 isolates of Neisseria meningitidis from invasive disease and healthy carriers. For each locus, alleles were assigned arbitrary numbers and dendrograms were constructed from the pairwise differences in multilocus allelic profiles by cluster analysis. The strain associations obtained were consistent with clonal groupings previously determined by multilocus enzyme electrophoresis. A subset of six gene fragments was chosen that retained the resolution and congruence achieved by using all 11 loci. Most isolates from hyper-virulent lineages of serogroups A, B, and C meningococci were identical for all loci or differed from the majority type at only a single locus. MLST using six loci therefore reliably identified the major meningococcal lineages associated with invasive disease. MLST can be applied to almost all bacterial species and other haploid organisms, including those that are difficult to cultivate. The overwhelming advantage of MLST over other molecular typing methods is that sequence data are truly portable between laboratories, permitting one expanding global database per species to be placed on a World-Wide Web site, thus enabling exchange of molecular typing data for global epidemiology via the Internet.
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            PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance

            Céline Nadon, Ivo Van Walle, Peter Gerner-Smidt … (2017)
            PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives. To meet the needs of real-time surveillance, the PulseNet International network will standardise subtyping via WGS using whole genome multilocus sequence typing (wgMLST), which delivers sufficiently high resolution and epidemiological concordance, plus unambiguous nomenclature for the purposes of surveillance. Standardised protocols, validation studies, quality control programmes, database and nomenclature development, and training should support the implementation and decentralisation of WGS. Ideally, WGS data collected for surveillance purposes should be publicly available, in real time where possible, respecting data protection policies. WGS data are suitable for surveillance and outbreak purposes and for answering scientific questions pertaining to source attribution, antimicrobial resistance, transmission patterns, and virulence, which will further enable the protection and improvement of public health with respect to food-borne disease.
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              Visualization of comparative genomic analyses by BLAST score ratio

              David Rasko, Garry Myers, Jacques Ravel (2005)
              Background The first microbial genome sequence, Haemophilus influenzae, was published in 1995. Since then, more than 400 microbial genome sequences have been completed or commenced. This massive influx of data provides the opportunity to obtain biological insights through comparative genomics. However few tools are available for this scale of comparative analysis. Results The BLAST Score Ratio (BSR) approach, implemented in a Perl script, classifies all putative peptides within three genomes using a measure of similarity based on the ratio of BLAST scores. The output of the BSR analysis enables global visualization of the degree of proteome similarity between all three genomes. Additional output enables the genomic synteny (conserved gene order) between each genome pair to be assessed. Furthermore, we extend this synteny analysis by overlaying BSR data as a color dimension, enabling visualization of the degree of similarity of the peptides being compared. Conclusions Combining the degree of similarity, synteny and annotation will allow rapid identification of conserved genomic regions as well as a number of common genomic rearrangements such as insertions, deletions and inversions. The script and example visualizations are available at: .
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                Author and article information

                Journal
                Journal ID (nlm-ta): Microb Genom
                Journal ID (iso-abbrev): Microb Genom
                Journal ID (publisher-id): MGen
                Title: Microbial Genomics
                Publisher: Microbiology Society
                ISSN (Electronic): 2057-5858
                Publication date Collection: March 2018
                Publication date (Electronic): 15 March 2018
                Publication date PMC-release: 15 March 2018
                Volume: 4
                Issue: 3
                Electronic Location Identifier: e000166
                Affiliations
                [ 1​ ]Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Lisbon, Portugal
                [ 2​ ]Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki , Helsinki, Finland
                [ 3​ ]School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev , Beer Sheva, Israel
                [ 4​ ]Public Health Services, Ministry of Health , Jerusalem, Israel
                Author notes
                *Correspondence: João André Carriço, jcarrico@ 123456fm.ul.pt
                Article
                Publisher ID: mgen000166
                DOI: 10.1099/mgen.0.000166
                PMC ID: 5885018
                PubMed ID: 29543149
                SO-VID: 4ea1f666-3f81-485e-be71-0472bea38804
                Copyright © © 2018 The Authors
                License:

                This is an open access article under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 24 October 2017
                Date accepted : 02 March 2018
                Funding
                Funded by: European Food Safety Authority
                Award ID: GP/EFSA/AFSCO/2015/01/CT2
                Funded by: European Food Safety Authority
                Award ID: GP/EFSA/AFSCO/2015/01/CT2
                Funded by: Fundos Europeus Estruturais e de Investimento
                Award ID: LISBOA-01-0145-FEDER-016417
                Funded by: FCT/ Scientific and Technological Research Council of Turkey
                Award ID: TUBITAK/0004/2014
                Categories
                Subject: Methods Paper
                Subject: Microbial Evolution and Epidemiology: Population Genomics
                Custom metadata
                OpenAccessEmbargo 0

                Keywords: chewbbaca,multilocus sequence typing,schema,gene-by-gene,allele calling
                Data availability:
                Keywords: chewbbaca, multilocus sequence typing, schema, gene-by-gene, allele calling

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