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

- Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groups
  
  D. R. Bogema, J. McKinnon, M. Liu, N. Hitchick, N. Miller, C. Venturini, J. Iredell, A. E. Darling, P. Roy Chowdury and S. P. Djordjevic
- Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont
  
  Ian Goodhead , Frances Blow , Philip Brownridge, Margaret Hughes, John Kenny, Ritesh Krishna, Lynn McLean , Pisut Pongchaikul , Rob Beynon and Alistair C. Darby
- Comparative genomic analysis identifies X-factor (haemin)-independent Haemophilus haemolyticus: a formal re-classification of 'Haemophilus intermedius'
  
  Tegan M. Harris, Erin P. Price, Derek S. Sarovich, Niels Nørskov-Lauritsen, Jemima Beissbarth, Anne B. Chang and Heidi C. Smith-Vaughan
- Population structure of KPC carbapenemase-producing Klebsiella pneumoniae in a long-term acute-care rehabilitation facility: identification of a new lineage of clonal group 101, associated with local hyperendemicity
  
  Fabio Arena , Vincenzo Di Pilato , Federica Vannetti , Laura Fabbri, Alberto Antonelli , Marco Coppi, Roberto Pupillo, Claudio Macchi and Gian Maria Rossolini
- Landscape of gene expression variation of natural isolates of Cryptococcus neoformans in response to biologically relevant stresses
  
  Chen-Hsin Yu , Yuan Chen , Christopher A. Desjardins , Jennifer L. Tenor, Dena L. Toffaletti, Charles Giamberardino, Anastasia Litvintseva, John R. Perfect and Christina A. Cuomo
- Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics
  
  Amol C. Shetty , John Mattick , Matthew Chung , Carrie McCracken, Anup Mahurkar , Scott G. Filler , Claire M. Fraser , David A. Rasko , Vincent M. Bruno and Julie C. Dunning Hotopp
- Genomic analysis of carbapenemase-producing Enterobacteriaceae in Queensland reveals widespread transmission of bla IMP-4 on an IncHI2 plasmid
  
  Leah W. Roberts , Elizabeth Catchpoole , Amy V. Jennison, Haakon Bergh, Anna Hume , Claire Heney , Narelle George, David L. Paterson , Mark A. Schembri , Scott A. Beatson and Patrick N. A. Harris
- Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28
  
  Keiji Nakamura , Kazunori Murase, Mitsuhiko P. Sato , Atsushi Toyoda , Takehiko Itoh , Jacques Georges Mainil, Denis Piérard, Shuji Yoshino, Keiko Kimata, Junko Isobe, Kazuko Seto, Yoshiki Etoh , Hiroshi Narimatsu, Shioko Saito, Jun Yatsuyanagi, Kenichi Lee , Sunao Iyoda, Makoto Ohnishi, Tadasuke Ooka , Yasuhiro Gotoh, Yoshitoshi Ogura and Tetsuya Hayashi
- Using genomics to understand meticillin- and vancomycin-resistant Staphylococcus aureus infections
  
  Stefano G. Giulieri , Steven Y. C. Tong and Deborah A. Williamson
- Tuberculosis in Liberia: high multidrug-resistance burden, transmission and diversity modelled by multiple importation events
  
  Mariana G. López , John B. Dogba , Manuela Torres-Puente , Galo A. Goig , Miguel Moreno-Molina , Luis M. Villamayor, Simeon Cadmus and Iñaki Comas
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Most cited articles

- 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
- Identification of Klebsiella capsule synthesis loci from whole genome data
  
  Kelly L. Wyres, Ryan R. Wick, Claire Gorrie, Adam Jenney, Rainer Follador, Nicholas R. Thomson and Kathryn E. Holt
- Completing bacterial genome assemblies with multiplex MinION sequencing
  
  Ryan R. Wick, Louise M. Judd, Claire L. Gorrie and Kathryn E. Holt
- Genome-scale rates of evolutionary change in bacteria
  
  Sebastian Duchêne, Kathryn E. Holt, François-Xavier Weill, Simon Le Hello, Jane Hawkey, David J. Edwards, Mathieu Fourment and Edward C. Holmes
- 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
- Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data
  
  Andrew J. Page, Nishadi De Silva, Martin Hunt, Michael A. Quail, Julian Parkhill, Simon R. Harris, Thomas D. Otto and Jacqueline A. Keane
- 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
- Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157:H7 strains causing severe human disease in the UK
  
  Timothy J. Dallman, Philip M. Ashton, Lisa Byrne, Neil T. Perry, Liljana Petrovska, Richard Ellis, Lesley Allison, Mary Hanson, Anne Holmes, George J. Gunn, Margo E. Chase-Topping, Mark E. J. Woolhouse, Kathie A. Grant, David L. Gally, John Wain and Claire Jenkins
- EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens
  
  Duo Peng and Rick Tarleton
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Microbial Genomics

Articles from the latest issue

Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groups

Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont

Comparative genomic analysis identifies X-factor (haemin)-independent Haemophilus haemolyticus: a formal re-classification of 'Haemophilus intermedius'

Population structure of KPC carbapenemase-producing Klebsiella pneumoniae in a long-term acute-care rehabilitation facility: identification of a new lineage of clonal group 101, associated with local hyperendemicity

Landscape of gene expression variation of natural isolates of Cryptococcus neoformans in response to biologically relevant stresses

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics

Genomic analysis of carbapenemase-producing Enterobacteriaceae in Queensland reveals widespread transmission of bla IMP-4 on an IncHI2 plasmid

Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28

Using genomics to understand meticillin- and vancomycin-resistant Staphylococcus aureus infections

Tuberculosis in Liberia: high multidrug-resistance burden, transmission and diversity modelled by multiple importation events

Most read this month

Most cited articles

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

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Identification of Klebsiella capsule synthesis loci from whole genome data

Completing bacterial genome assemblies with multiplex MinION sequencing

Genome-scale rates of evolutionary change in bacteria

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data

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

Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157:H7 strains causing severe human disease in the UK

EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens