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Highlights from infectious disease genomics

Genome Medicine Collection

New Content ItemNext-generation sequencing approaches are rapidly advancing our understanding of pathogens and clinical management of infectious diseases. This collection showcases recent Genome Medicine articles that have made exciting contributions within this field. Articles in this collection cover insights from whole-genome sequencing into pathogen evolution, transmission, and drug resistance, as well as advances in clinical diagnostics of both viral and bacterial pathogens and treatment strategies. Additionally, it features articles focusing on host immune response and protection against infection, from a genomics perspective.

  1. Research

    Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom

    Residents of long-term care facilities (LTCF) may have high carriage rates of multidrug-resistant pathogens, but are not currently included in surveillance programmes for antimicrobial resistance or healthcare...

    Hayley J. Brodrick, Kathy E. Raven, Teemu Kallonen, Dorota Jamrozy, Beth Blane, Nicholas M. Brown, Veronique Martin, M. Estée Török, Julian Parkhill and Sharon J. Peacock

    Genome Medicine 2017 9:70

    Published on: 25 July 2017

  2. Research

    High-dimensional assessment of B-cell responses to quadrivalent meningococcal conjugate and plain polysaccharide vaccine

    Neisseria meningitidis is a globally important cause of meningitis and septicaemia. Twelve capsular groups of meningococci are known, and quadrivalent vaccines against four of these (A...

    Daniel O’Connor, Elizabeth A. Clutterbuck, Amber J. Thompson, Matthew D. Snape, Maheshi N. Ramasamy, Dominic F. Kelly and Andrew J. Pollard

    Genome Medicine 2017 9:11

    Published on: 30 January 2017

  3. Research

    The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs

    The emergence of resistance to anti-tuberculosis drugs is a serious and growing threat to public health. Next-generation sequencing is rapidly gaining traction as a diagnostic tool for investigating drug resis...

    Jody Phelan, Denise M. O’Sullivan, Diana Machado, Jorge Ramos, Alexandra S. Whale, Justin O’Grady, Keertan Dheda, Susana Campino, Ruth McNerney, Miguel Viveiros, Jim F. Huggett and Taane G. Clark

    Genome Medicine 2016 8:132

    Published on: 22 December 2016

  4. Research

    Next-generation sequencing diagnostics of bacteremia in septic patients

    Bloodstream infections remain one of the major challenges in intensive care units, leading to sepsis or even septic shock in many cases. Due to the lack of timely diagnostic approaches with sufficient sensitiv...

    Silke Grumaz, Philip Stevens, Christian Grumaz, Sebastian O. Decker, Markus A. Weigand, Stefan Hofer, Thorsten Brenner, Arndt von Haeseler and Kai Sohn

    Genome Medicine 2016 8:73

    Published on: 1 July 2016

  5. Research

    B-cell repertoire dynamics after sequential hepatitis B vaccination and evidence for cross-reactive B-cell activation

    A diverse B-cell repertoire is essential for recognition and response to infectious and vaccine antigens. High-throughput sequencing of B-cell receptor (BCR) genes can now be used to study the B-cell repertoir...

    Jacob D. Galson, Johannes Trück, Elizabeth A. Clutterbuck, Anna Fowler, Vincenzo Cerundolo, Andrew J. Pollard, Gerton Lunter and Dominic F. Kelly

    Genome Medicine 2016 8:68

    Published on: 16 June 2016

    The Erratum to this article has been published in Genome Medicine 2016 8:81

  6. Review

    Microbiome mediation of infections in the cancer setting

    Infections encountered in the cancer setting may arise from intensive cancer treatments or may result from the cancer itself, leading to risk of infections through immune compromise, disruption of anatomic bar...

    Ying Taur and Eric G. Pamer

    Genome Medicine 2016 8:40

    Published on: 18 April 2016

  7. Research

    Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus

    Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common healthcare-associated pathogens. To examine the role of inter-hospital patient sharing on MRSA transmission, a previous study collected...

    Hsiao-Han Chang, Janina Dordel, Tjibbe Donker, Colin J. Worby, Edward J. Feil, William P. Hanage, Stephen D. Bentley, Susan S. Huang and Marc Lipsitch

    Genome Medicine 2016 8:18

    Published on: 13 February 2016

  8. Research

    Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network

    Bacterial whole-genome sequencing (WGS) has the potential to identify reservoirs of multidrug-resistant organisms and transmission of these pathogens across healthcare networks. We used WGS to define transmiss...

    Hayley J. Brodrick, Kathy E. Raven, Ewan M. Harrison, Beth Blane, Sandra Reuter, M. Estée Török, Julian Parkhill and Sharon J. Peacock

    Genome Medicine 2016 8:4

    Published on: 12 January 2016

  9. Research

    Longitudinal analysis of the peripheral B cell repertoire reveals unique effects of immunization with a new influenza virus strain

    Despite the potential to produce antibodies that can neutralize different virus (heterotypic neutralization), there is no knowledge of why vaccination against influenza induces protection predominantly against...

    Bernardo Cortina-Ceballos, Elizabeth Ernestina Godoy-Lozano, Juan Téllez-Sosa, Marbella Ovilla-Muñoz, Hugo Sámano-Sánchez, Andrés Aguilar-Salgado, Rosa Elena Gómez-Barreto, Humberto Valdovinos-Torres, Irma López-Martínez, Rodrigo Aparicio-Antonio, Mario H. Rodríguez and Jesús Martínez-Barnetche

    Genome Medicine 2015 7:124

    Published on: 25 November 2015

  10. Method

    Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

    We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly developed, ...

    Alexander L. Greninger, Samia N. Naccache, Scot Federman, Guixia Yu, Placide Mbala, Vanessa Bres, Doug Stryke, Jerome Bouquet, Sneha Somasekar, Jeffrey M. Linnen, Roger Dodd, Prime Mulembakani, Bradley S. Schneider, Jean-Jacques Muyembe-Tamfum, Susan L. Stramer and Charles Y. Chiu

    Genome Medicine 2015 7:99

    Published on: 29 September 2015

  11. Method

    Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

    Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequenci...

    Francesc Coll, Ruth McNerney, Mark D Preston, José Afonso Guerra-Assunção, Andrew Warry, Grant Hill-Cawthorne, Kim Mallard, Mridul Nair, Anabela Miranda, Adriana Alves, João Perdigão, Miguel Viveiros, Isabel Portugal, Zahra Hasan, Rumina Hasan, Judith R Glynn…

    Genome Medicine 2015 7:51

    Published on: 27 May 2015

  12. Research

    Transcriptional profiling defines dynamics of parasite tissue sequestration during malaria infection

    During intra-erythrocytic development, late asexually replicating Plasmodium falciparum parasites sequester from peripheral circulation. This facilitates chronic infection and is linked to severe disease and orga...

    Karell G Pelle, Keunyoung Oh, Kathrin Buchholz, Vagheesh Narasimhan, Regina Joice, Danny A Milner, Nicolas MB Brancucci, Siyuan Ma, Till S Voss, Ken Ketman, Karl B Seydel, Terrie E Taylor, Natasha S Barteneva, Curtis Huttenhower and Matthias Marti

    Genome Medicine 2015 7:19

    Published on: 27 February 2015

  13. Research

    Plasmodium falciparumgene expression measured directly from tissue during human infection

    During the latter half of the natural 48-h intraerythrocytic life cycle of human Plasmodium falciparum infection, parasites sequester deep in endothelium of tissues, away from the spleen and inaccessible to perip...

    Daria Van Tyne, Yan Tan, Johanna P Daily, Steve Kamiza, Karl Seydel, Terrie Taylor, Jill P Mesirov, Dyann F Wirth and Danny A Milner

    Genome Medicine 2014 6:110

    Published on: 29 November 2014

  14. Research

    Next generation sequencing analysis of nine Corynebacterium ulcerans isolates reveals zoonotic transmission and a novel putative diphtheria toxin-encoding pathogenicity island

    Toxigenic Corynebacterium ulcerans can cause a diphtheria-like illness in humans and have been found in domestic animals, which were suspected to serve as reservoirs for a zoonotic transmission. Additionally, tox...

    Dominik M Meinel, Gabriele Margos, Regina Konrad, Stefan Krebs, Helmut Blum and Andreas Sing

    Genome Medicine 2014 6:113

    Published on: 28 November 2014

  15. Research

    An integrated transcriptome and expressed variant analysis of sepsis survival and death

    Sepsis, a leading cause of morbidity and mortality, is not a homogeneous disease but rather a syndrome encompassing many heterogeneous pathophysiologies. Patient factors including genetics predispose to poor o...

    Ephraim L Tsalik, Raymond J Langley, Darrell L Dinwiddie, Neil A Miller, Byunggil Yoo, Jennifer C van Velkinburgh, Laurie D Smith, Isabella Thiffault, Anja K Jaehne, Ashlee M Valente, Ricardo Henao, Xin Yuan, Seth W Glickman, Brandon J Rice, Micah T McClain, Lawrence Carin…

    Genome Medicine 2014 6:111

    Published on: 26 November 2014

  16. Research

    Transcriptional fingerprints of antigen-presenting cell subsets in the human vaginal mucosa and skin reflect tissue-specific immune microenvironments

    Dendritic cells localize throughout the body, where they can sense and capture invading pathogens to induce protective immunity. Hence, harnessing the biology of tissue-resident dendritic cells is fundamental ...

    Dorothée Duluc, Romain Banchereau, Julien Gannevat, Luann Thompson-Snipes, Jean-Philippe Blanck, Sandra Zurawski, Gerard Zurawski, Seunghee Hong, Jose Rossello-Urgell, Virginia Pascual, Nicole Baldwin, Jack Stecher, Michael Carley, Muriel Boreham and SangKon Oh

    Genome Medicine 2014 6:98

    Published on: 25 November 2014

  17. Software

    SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

    Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significa...

    Michael Inouye, Harriet Dashnow, Lesley-Ann Raven, Mark B Schultz, Bernard J Pope, Takehiro Tomita, Justin Zobel and Kathryn E Holt

    Genome Medicine 2014 6:90

    Published on: 20 November 2014

  18. Method

    A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens

    Whole genome sequencing is increasingly used to study phenotypic variation among infectious pathogens and to evaluate their relative transmissibility, virulence, and immunogenicity. To date, relatively little ...

    Maha R Farhat, B Jesse Shapiro, Samuel K Sheppard, Caroline Colijn and Megan Murray

    Genome Medicine 2014 6:101

    Published on: 15 November 2014

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