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Genomics of infectious diseases special issue

Guest Editors: George Weinstock and Sharon Peacock

Whole-genome sequences are now achievable within days and available for multiple pathogens, including those that cause neglected tropical diseases, which has advanced our understanding of the biology and evolution of pathogens. Crucially, such research has enabled important advances in the clinical management of infectious diseases, and continues to guide public health interventions worldwide.

Here, Genome Biology and Genome Medicine take stock of where we are now, with a collection of articles that discuss different aspects of the genomics of infectious diseases in human populations, including the progress made towards their eradication, and the remaining challenges in terms of both fundamental science and clinical management.

  1. Method

    FRESCo: finding regions of excess synonymous constraint in diverse viruses

    The increasing availability of sequence data for many viruses provides power to detect regions under unusual evolutionary constraint at a high resolution. One approach leverages the synonymous substitution rat...

    Rachel S Sealfon, Michael F Lin, Irwin Jungreis, Maxim Y Wolf, Manolis Kellis and Pardis C Sabeti

    Genome Biology 2015 16:38

    Published on: 17 February 2015

  2. 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

  3. 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

  4. 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

  5. Review

    Drug resistance genomics of the antimalarial drug artemisinin

    Across the globe, over 200 million annual malaria infections result in up to 660,000 deaths, 77% of which occur in children under the age of five years. Although prevention is important, malaria deaths are typ...

    Elizabeth A Winzeler and Micah J Manary

    Genome Biology 2014 15:544

    Published on: 25 November 2014

  6. Research

    Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity

    Ebolaviruses cause a severe and often fatal haemorrhagic fever in humans, with some species such as Ebola virus having case fatality rates approaching 90%. Currently, the worst Ebola virus outbreak since the d...

    Stuart D Dowall, David A Matthews, Isabel García-Dorival, Irene Taylor, John Kenny, Christiane Hertz-Fowler, Neil Hall, Kara Corbin-Lickfett, Cyril Empig, Kyle Schlunegger, John N Barr, Miles W Carroll, Roger Hewson and Julian A Hiscox

    Genome Biology 2014 15:540

    Published on: 22 November 2014

  7. Research

    The genome of the sparganosis tapeworm Spirometra erinaceieuropaeiisolated from the biopsy of a migrating brain lesion

    Sparganosis is an infection with a larval Diphyllobothriidea tapeworm. From a rare cerebral case presented at a clinic in the UK, DNA was recovered from a biopsy sample and used to determine the causative spec...

    Hayley M Bennett, Hoi Ping Mok, Effrossyni Gkrania-Klotsas, Isheng J Tsai, Eleanor J Stanley, Nagui M Antoun, Avril Coghlan, Bhavana Harsha, Alessandra Traini, Diogo M Ribeiro, Sascha Steinbiss, Sebastian B Lucas, Kieren SJ Allinson, Stephen J Price, Thomas S Santarius, Andrew J Carmichael…

    Genome Biology 2014 15:510

    Published on: 21 November 2014

  8. 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

  9. Research

    Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumanniiin Birmingham, England

    Multidrug-resistant Acinetobacter baumannii commonly causes hospital outbreaks. However, within an outbreak, it can be difficult to identify the routes of cross-infection rapidly and accurately enough to inform i...

    Mihail R Halachev, Jacqueline Z-M Chan, Chrystala I Constantinidou, Nicola Cumley, Craig Bradley, Matthew Smith-Banks, Beryl Oppenheim and Mark J Pallen

    Genome Medicine 2014 6:70

    Published on: 20 November 2014

  10. Software

    YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens

    The design of effective antimicrobial therapies for serious eukaryotic pathogens requires a clear understanding of their highly variable genomes. To facilitate analysis of copy number variations, single nucleo...

    Darren A Abbey, Jason Funt, Mor N Lurie-Weinberger, Dawn A Thompson, Aviv Regev, Chad L Myers and Judith Berman

    Genome Medicine 2014 6:100

    Published on: 20 November 2014

  11. Research

    Global gene expression profiling identifies new therapeutic targets in acute Kawasaki disease

    Global gene expression profiling can provide insight into the underlying pathophysiology of disease processes. Kawasaki disease (KD) is an acute, self-limited vasculitis whose etiology remains unknown. Althoug...

    Long Truong Hoang, Chisato Shimizu, Ling Ling, Ahmad Nazri Mohamed Naim, Chiea Chuen Khor, Adriana H Tremoulet, Victoria Wright, Michael Levin, Martin L Hibberd and Jane C Burns

    Genome Medicine 2014 6:541

    Published on: 20 November 2014

  12. Research highlight

    Stopping outbreaks with real-time genomic epidemiology

    One of the most successful public health applications of next-generation sequencing is whole-genome sequencing of pathogens to not only detect and characterize outbreaks, but also to inform outbreak management...

    Patrick Tang and Jennifer L Gardy

    Genome Medicine 2014 6:104

    Published on: 20 November 2014

  13. Method

    BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads

    We present a method for obtaining long haplotypes, of over 3 kb in length, using a short-read sequencer, Barcode-directed Assembly for Extra-long Sequences (BAsE-Seq). BAsE-Seq relies on transposing a template...

    Lewis Z Hong, Shuzhen Hong, Han Teng Wong, Pauline PK Aw, Yan Cheng, Andreas Wilm, Paola F de Sessions, Seng Gee Lim, Niranjan Nagarajan, Martin L Hibberd, Stephen R Quake and William F Burkholder

    Genome Biology 2014 15:517

    Published on: 19 November 2014

  14. Editorial

    Microbial sequencing to improve individual and population health

    Recent advances in sequencing technologies are changing the face of infectious disease investigation and control. Personalized anti-infective therapies and surveillance of emergent pathogen outbreaks are just ...

    Sharon J Peacock and George M Weinstock

    Genome Medicine 2014 6:103

    Published on: 19 November 2014

  15. Opinion

    Genomics and infectious disease: a call to identify the ethical, legal and social implications for public health and clinical practice

    Advances in genomics are contributing to the development of more effective, personalized approaches to the prevention and treatment of infectious diseases. Genetic sequencing technologies are furthering our un...

    Gail Geller, Rachel Dvoskin, Chloe L Thio, Priya Duggal, Michelle H Lewis, Theodore C Bailey, Andrea Sutherland, Daniel A Salmon and Jeffrey P Kahn

    Genome Medicine 2014 6:106

    Published on: 18 November 2014

  16. Method

    Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples

    We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targe...

    Christian B Matranga, Kristian G Andersen, Sarah Winnicki, Michele Busby, Adrianne D Gladden, Ryan Tewhey, Matthew Stremlau, Aaron Berlin, Stephen K Gire, Eleina England, Lina M Moses, Tarjei S Mikkelsen, Ikponmwonsa Odia, Philomena E Ehiane, Onikepe Folarin, Augustine Goba…

    Genome Biology 2014 15:519

    Published on: 18 November 2014

  17. 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

  18. Research

    Proteomics informed by transcriptomics reveals Hendra virus sensitizes bat cells to TRAIL-mediated apoptosis

    Bats are a major reservoir of emerging infectious viruses. Many of these viruses are highly pathogenic to humans however bats remain asymptomatic. The mechanism by which bats control viral replication is unkno...

    James W Wynne, Brian J Shiell, Glenn A Marsh, Victoria Boyd, Jennifer A Harper, Kate Heesom, Paul Monaghan, Peng Zhou, Jean Payne, Reuben Klein, Shawn Todd, Lawrence Mok, Diane Green, John Bingham, Mary Tachedjian, Michelle L Baker…

    Genome Biology 2014 15:532

    Published on: 15 November 2014

  19. Review

    Engineering the control of mosquito-borne infectious diseases

    Recent advances in genetic engineering are bringing new promise for controlling mosquito populations that transmit deadly pathogens. Here we discuss past and current efforts to engineer mosquito strains that a...

    Paolo Gabrieli, Andrea Smidler and Flaminia Catteruccia

    Genome Biology 2014 15:535

    Published on: 15 November 2014

  20. Research

    The conjunctival microbiome in health and trachomatous disease: a case control study

    Trachoma, caused by Chlamydia trachomatis, remains the worlds leading infectious cause of blindness. Repeated ocular infection during childhood leads to scarring of the conjunctiva, in-turning of the eyelashes (t...

    Yanjiao Zhou, Martin J Holland, Pateh Makalo, Hassan Joof, Chrissy h Roberts, David CW Mabey, Robin L Bailey, Matthew J Burton, George M Weinstock and Sarah E Burr

    Genome Medicine 2014 6:99

    Published on: 15 November 2014

  21. Research

    A genomic and evolutionary approach reveals non-genetic drug resistance in malaria

    Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis wi...

    Jonathan D Herman, Daniel P Rice, Ulf Ribacke, Jacob Silterra, Amy A Deik, Eli L Moss, Kate M Broadbent, Daniel E Neafsey, Michael M Desai, Clary B Clish, Ralph Mazitschek and Dyann F Wirth

    Genome Biology 2014 15:511

    Published on: 14 November 2014

  22. Research highlight

    The road to drug resistance in Mycobacterium tuberculosis

    Sequencing of serial isolates of extensively drug-resistant tuberculosis highlights how drug resistance develops within a single patient and reveals unexpected levels of pathogen diversity.

    Anastasia Koch and Robert John Wilkinson

    Genome Biology 2014 15:520

    Published on: 13 November 2014

  23. Research highlight

    A CRISPR design for next-generation antimicrobials

    Two recent publications have demonstrated how delivering CRISPR nucleases provides a promising solution to the growing problem of bacterial antibiotic resistance.

    Chase L Beisel, Ahmed A Gomaa and Rodolphe Barrangou

    Genome Biology 2014 15:516

    Published on: 8 November 2014

  24. Research

    Whole genome sequencing of SIV-infected macaques identifies candidate loci that may contribute to host control of virus replication

    A small percentage of human immunodeficiency virus (HIV)-infected people and simian immunodeficiency virus (SIV)-infected macaques control virus replication without antiretroviral treatment. The major determin...

    Adam J Ericsen, Gabriel J Starrett, Justin M Greene, Michael Lauck, Muthuswamy Raveendran, David Rio Deiros, Mariel S Mohns, Nicolas Vince, Brian T Cain, Ngoc H Pham, Jason T Weinfurter, Adam L Bailey, Melisa L Budde, Roger W Wiseman, Richard Gibbs, Donna Muzny…

    Genome Biology 2014 15:478

    Published on: 7 November 2014

  25. Research

    Evolution of extensively drug-resistant Mycobacterium tuberculosisfrom a susceptible ancestor in a single patient

    Mycobacterium tuberculosis is characterized by a low mutation rate and a lack of genetic recombination. Yet, the rise of extensively resistant strains paints a picture of a microbe with an impressive adaptive pot...

    Vegard Eldholm, Gunnstein Norheim, Bent von der Lippe, Wibeke Kinander, Ulf R Dahle, Dominique A Caugant, Turid Mannsåker, Anne Torunn Mengshoel, Anne Ma Dyrhol-Riise and Francois Balloux

    Genome Biology 2014 15:490

    Published on: 7 November 2014

  26. Comment

    Empowering African genomics for infectious disease control

    At present, African scientists can only participate minimally in the genomics revolution that is transforming the understanding, surveillance and clinical treatment of infectious diseases. We discuss new initi...

    Onikepe A Folarin, Anise N Happi and Christian T Happi

    Genome Biology 2014 15:515

    Published on: 7 November 2014

  27. Research

    Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires’ disease

    The genus Legionella comprises over 60 species. However, L. pneumophila and L. longbeachae alone cause over 95% of Legionnaires’ disease. To identify the genetic bases underlying the different capacities to cause...

    Laura Gomez-Valero, Christophe Rusniok, Monica Rolando, Mario Neou, Delphine Dervins-Ravault, Jasmin Demirtas, Zoe Rouy, Robert J Moore, Honglei Chen, Nicola K Petty, Sophie Jarraud, Jerome Etienne, Michael Steinert, Klaus Heuner, Simonetta Gribaldo, Claudine Médigue…

    Genome Biology 2014 15:505

    Published on: 3 November 2014

  28. Research

    Staphylococcus aureusgene expression in a rat model of infective endocarditis

    Diabetes mellitus is a frequent underlying comorbidity in patients with Staphylococcus aureus endocarditis, and it represents a risk factor for complications and a negative outcome. The pathogenesis of staphyloco...

    Frank Hanses, Christelle Roux, Paul M Dunman, Bernd Salzberger and Jean C Lee

    Genome Medicine 2014 6:93

    Published on: 3 November 2014

  29. Research

    Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network

    Mycobacterium tuberculosis senses and responds to the shifting and hostile landscape of the host. To characterize the underlying intertwined gene regulatory network governed by approximately 200 transcription fac...

    Tige R Rustad, Kyle J Minch, Shuyi Ma, Jessica K Winkler, Samuel Hobbs, Mark Hickey, William Brabant, Serdar Turkarslan, Nathan D Price, Nitin S Baliga and David R Sherman

    Genome Biology 2014 15:502

    Published on: 3 November 2014

  30. Research

    Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires’ disease outbreak

    Legionnaires’ disease is a severe form of pneumonia caused by the environmental bacterium Legionella pneumophila. Outbreaks commonly affect people with known risk factors, but the genetic and pathogenic complexit...

    Paul R McAdam, Charles W Vander Broek, Diane SJ Lindsay, Melissa J Ward, Mary F Hanson, Michael Gillies, Mick Watson, Joanne M Stevens, Giles F Edwards and J Ross Fitzgerald

    Genome Biology 2014 15:504

    Published on: 3 November 2014

  31. Research

    Genome-wide RIP-Chip analysis of translational repressor-bound mRNAs in the Plasmodium gametocyte

    Following fertilization, the early proteomes of metazoans are defined by the translation of stored but repressed transcripts; further embryonic development relies on de novo transcription of the zygotic genome. D...

    Ana Guerreiro, Elena Deligianni, Jorge M Santos, Patricia AGC Silva, Christos Louis, Arnab Pain, Chris J Janse, Blandine Franke-Fayard, Celine K Carret, Inga Siden-Kiamos and Gunnar R Mair

    Genome Biology 2014 15:493

    Published on: 3 November 2014