Team III Comparative Genomics Group

Team 3: Comparative Genomics

• File:Comparative Genomics - Team 3 Background and Strategy.pptx.pdf
• File:Comparative Genomics - Team 3 Results.pptx.pdf

Team Members: Swetha Singu, Ruize Yang, Deepali Kundnani, Gulay Bengu Ulukaya, Yuhua Zhang, Jie Zhou

Introduction

Background

Comparative genomics is a field of biological research in which different organisms are compared for their genomic features like the DNA sequence, genes, order of genes and other genomic structural landmarks. This comparative analysis can reveal many insights, such as disease outbreak strains, sporadic strains, evolutionary lineages and genetic variations to name a few. Our group was given 50 different isolates for which genome assembly, gene prediction and functional annotation was performed and the species was identified as Listeria Monocytogenes.

Objectives

Identify the outbreak strains from the sporadic strains for the given isolates Analyze the source of the outbreak using the epidemiological data provided. Determine the virulence and antibiotic resistance profiles of the outbreak isolates. Recommendation for outbreak response and classes of antibiotics to prescribe and to avoid.

Information at hand

Data we have?

Pipeline

pipeline

Approaches

We use five different bioinformatic tools from different levels to compare the 50 isolates.

ANI

introduction of ANI, what level is the method, and the tools used, input and output, general results

MLST

StringMLST, ChewBBACA

SNP-based Typing

kSNP

Pan-genome analysis

Roary, BPGA

References

Filliol I, et al. Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J. Bacteriol. 2006;188:759–772. doi: 10.1128/JB.188.2.759-772.2006.

Adam D. Leaché1 and Jamie R. Oaks2, The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics. Annual Review of Ecology, Evolution, and Systematics. 2017; Vol. 48:69-84. https://doi.org/10.1146/annurev-ecolsys-110316-022645

Shea N Gardner, Tom Slezak, Barry G. Hall, kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome, Bioinformatics, Volume 31, Issue 17, 1 September 2015, Pages 2877–2878, https://doi.org/10.1093/bioinformatics/btv271

Maiden, Martin C J. “Multilocus Sequence Typing of Bacteria.” Annual Review of Microbiology, U.S. National Library of Medicine, 2006, www.ncbi.nlm.nih.gov/pubmed/16774461.

Silva, Mickael, et al. “ChewBBACA: A Complete Suite for Gene-by-Gene Schema Creation and Strain Identification.” Microbial Genomics, Microbiology Society, Mar. 2018, www.ncbi.nlm.nih.gov/pmc/articles/PMC5885018/.

“MentaLiST.” OmicX, omictools.com/mentalist-tool. Feijao, Pedro, et al. “MentaLiST – A Fast MLST Caller for Large MLST Schemes.” BioRxiv, Cold Spring Harbor Laboratory, 1 Jan. 2017, www.biorxiv.org/content/10.1101/172858v2.

Kim, Yeji, et al. “Current Status of Pan-Genome Analysis for Pathogenic Bacteria.” Current Opinion in Biotechnology, vol. 63, 2020, pp. 54–62., doi:10.1016/j.copbio.2019.12.001.

Page, Andrew J., et al. “Roary: Rapid Large-Scale Prokaryote Pan Genome Analysis.” Bioinformatics, vol. 31, no. 22, 2015, pp. 3691–3693., doi:10.1093/bioinformatics/btv421.

Chaudhari, Narendrakumar M., et al. “BPGA- an Ultra-Fast Pan-Genome Analysis Pipeline.” Scientific Reports, vol. 6, no. 1, 2016, doi:10.1038/srep24373.

Valentina Galata, Tobias Fehlmann, Christina Backes, Andreas Keller, PLSDB: a resource of complete bacterial plasmids, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D195–D202

Hunt, Martin et al. “ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads.” Microbial genomics vol. 3,10 e000131. 4 Sep. 2017, doi:10.1099/mgen.0.000131 Annaleise Wilson et al. “Phenotypic and Genotypic

Analysis of Antimicrobial Resistance among Listeria monocytogenes Isolated from Australian Food Production Chains”. Feb 9, 2018. Genes  doi: 10.3390/genes9020080

Clementine Henri et al “An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes”Front. Microbiol., 29 November 2017 | https://doi.org/10.3389/fmicb.2017.02351

Yi Chen et al “Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes” Appl Environ Microbiology, 2016 Oct 15 doi: 10.1128/AEM.01532-16

"Identification of acquired antimicrobial resistance genes", Zankari et al 2012, PMID: 22782487