Microbial Genomics

Microbial Genomics

E-ISSN: 2057-5858

Microbial Genomics is the open access journal of choice for pioneering research in genomics in microbial life. We welcome articles showing novel insights, exciting new applications, or innovative approaches to analysis using genomic data, as well as articles developing our understanding of microbial genomics, from large, long-term studies on microbial evolution and epidemiology to studies with immediate clinical or environmental relevance. More

Editorial Board
Editor-in-Chief: Professor Kathryn Holt, Monash University, Australia and London School of Hygiene and Tropical Medicine, UK
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Journal status	Active

Articles from the latest issue Latest Articles Rss Feed

- Accelerating surveillance and research of antimicrobial resistance – an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences
  
  Sébastien Matamoros , Rene S. Hendriksen , Bálint Ármin Pataki , Nima Pakseresht, Marc Rossello, Nicole Silvester, Clara Amid, Frank M. Aarestrup, Marion Koopmans, Guy Cochrane , Istvan Csabai , Ole Lund, Constance Schultsz and The COMPARE ML-AMR group
- Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico
  
  Enzo Guerrero-Araya , Claudio Meneses , Eduardo Castro-Nallar , Ana M. Guzmán D., Manuel Álvarez-Lobos , Carlos Quesada-Gómez , Daniel Paredes-Sabja and César Rodríguez
- Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates
  
  Rebecca A. Gladstone , Stephanie W. Lo , Richard Goater, Corin Yeats , Ben Taylor , James Hadfield, John A. Lees , Nicholas J. Croucher, Andries J. van Tonder , Leon J. Bentley, Fu Xiang Quah , Anne J. Blaschke , Nicole L. Pershing , Carrie L. Byington, Veeraraghavan Balaji, Waleria Hryniewicz, Betuel Sigauque, K.L. Ravikumar, Samanta Cristine Grassi Almeida, Theresa J. Ochoa , Pak Leung Ho , Mignon du Plessis , Kedibone M. Ndlangisa, Jennifer E. Cornick, Brenda Kwambana-Adams , Rachel Benisty, Susan A. Nzenze, Shabir A. Madhi, Paulina A. Hawkins, Andrew J. Pollard , Dean B. Everett, Martin Antonio, Ron Dagan, Keith P. Klugman, Anne von Gottberg , Benjamin J. Metcalf , Yuan Li, Bernard W. Beall, Lesley McGee , Robert F. Breiman, David M. Aanensen, Stephen D. Bentley and The Global Pneumococcal Sequencing Consortium
- Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid
  
  Patricia Alba , Pimlapas Leekitcharoenphon , Virginia Carfora , Roberta Amoruso, Gessica Cordaro, Paola Di Matteo, Angela Ianzano, Manuela Iurescia , Elena L. Diaconu , ENGAGE-EURL-AR Network Study Group, Susanne K. Pedersen , Beatriz Guerra, Rene S. Hendriksen , Alessia Franco and Antonio Battisti
- Meningococcal core and accessory phasomes vary by clonal complex
  
  Joseph J. Wanford, Jonathan C. Holmes, Christopher D. Bayliss and Luke R. Green
- prewas: data pre-processing for more informative bacterial GWAS
  
  Katie Saund , Zena Lapp , Stephanie N. Thiede , Ali Pirani and Evan S. Snitkin
- Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae
  
  Ines Bleriot, Rocío Trastoy , Lucia Blasco , Felipe Fernández-Cuenca, Antón Ambroa , Laura Fernández-García , Olga Pacios , Elena Perez-Nadales, Julian Torre-Cisneros, Jesús Oteo-Iglesias , Ferran Navarro , Elisenda Miró , Alvaro Pascual , German Bou, Luis Martínez-Martínez and Maria Tomas
- Antibiotic resistance in Pseudomonas aeruginosa and adaptation to complex dynamic environments
  
  Lea M. Sommer , Helle K. Johansen and Søren Molin
- Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital
  
  Priyanka Hastak , Max L. Cummins , Thomas Gottlieb, Elaine Cheong, John Merlino, Garry S. A. Myers , Steven P. Djordjevic and Piklu Roy Chowdhury
- Identification of integrative and conjugative elements in pathogenic and commensal Neisseriaceae species via genomic distributions of DNA uptake sequence dialects
  
  Alex Hughes-Games , Adam P. Roberts , Sean A. Davis and Darryl J. Hill
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Most cited this month Most Cited RSS feed

- SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
  
  Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane and Simon R. Harris
- ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
  
  Martin Hunt, Alison E Mather, Leonor Sánchez-Busó, Andrew J Page, Julian Parkhill, Jacqueline A Keane and Simon R Harris
- Completing bacterial genome assemblies with multiplex MinION sequencing
  
  Ryan R. Wick, Louise M. Judd, Claire L. Gorrie and Kathryn E. Holt
- Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes
  
  Paul O. Sheridan, Jennifer C. Martin, Trevor D. Lawley, Hilary P. Browne, Hugh M. B. Harris, Annick Bernalier-Donadille, Sylvia H. Duncan, Paul W. O'Toole, Karen P. Scott and Harry J. Flint
- NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats
  
  Jason W. Sahl, Darrin Lemmer, Jason Travis, James M. Schupp, John D. Gillece, Maliha Aziz, Elizabeth M. Driebe, Kevin P. Drees, Nathan D. Hicks, Charles Hall Davis Williamson, Crystal M. Hepp, David Earl Smith, Chandler Roe, David M. Engelthaler, David M. Wagner and Paul Keim
- chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
  
  Mickael Silva, Miguel P. Machado, Diogo N. Silva, Mirko Rossi, Jacob Moran-Gilad, Sergio Santos, Mario Ramirez and João André Carriço
- SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology
  
  Aaron Petkau, Philip Mabon, Cameron Sieffert, Natalie C. Knox, Jennifer Cabral, Mariam Iskander, Mark Iskander, Kelly Weedmark, Rahat Zaheer, Lee S. Katz, Celine Nadon, Aleisha Reimer, Eduardo Taboada, Robert G. Beiko, William Hsiao, Fiona Brinkman, Morag Graham and Gary Van Domselaar
- On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data
  
  Sergio Arredondo-Alonso, Rob J. Willems, Willem van Schaik and Anita C. Schürch
- Microreact: visualizing and sharing data for genomic epidemiology and phylogeography
  
  Silvia Argimón, Khalil Abudahab, Richard J. E. Goater, Artemij Fedosejev, Jyothish Bhai, Corinna Glasner, Edward J. Feil, Matthew T. G. Holden, Corin A. Yeats, Hajo Grundmann, Brian G. Spratt and David M. Aanensen
- Quantitative assessment of insertion sequence impact on bacterial genome architecture
  
  Mark D. Adams, Brian Bishop and Meredith S. Wright
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Microbial Genomics

Articles from the latest issue Latest Articles Rss Feed

Accelerating surveillance and research of antimicrobial resistance – an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences

Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico

Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates

Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid

Meningococcal core and accessory phasomes vary by clonal complex

prewas: data pre-processing for more informative bacterial GWAS

Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae

Antibiotic resistance in Pseudomonas aeruginosa and adaptation to complex dynamic environments

Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital

Identification of integrative and conjugative elements in pathogenic and commensal Neisseriaceae species via genomic distributions of DNA uptake sequence dialects

Most read this month

Most cited this month Most Cited RSS feed

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Completing bacterial genome assemblies with multiplex MinION sequencing

Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes

NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats

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

SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology

On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

Quantitative assessment of insertion sequence impact on bacterial genome architecture