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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. Content type: Method

    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...

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

    Citation: Genome Biology 2015 16:38

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  2. Content type: Research

    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...

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

    Citation: Genome Medicine 2014 6:110

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  3. Content type: Review

    The current therapeutic arsenal against viral infections remains limited, with often poor efficacy and incomplete coverage, and appears inadequate to face the emergence of drug resistance. Our understanding of...

    Authors: Benoît de Chassey, Laurène Meyniel-Schicklin, Jacky Vonderscher, Patrice André and Vincent Lotteau

    Citation: Genome Medicine 2014 6:115

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  4. Content type: Research

    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...

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

    Citation: Genome Medicine 2014 6:113

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  5. Content type: Method

    Bacteria have been shown to generate constant genetic variation in a process termed phase variation. We present a tool based on whole genome sequencing that allows detection and quantification of coexisting ge...

    Authors: Amir Goldberg, Ofer Fridman, Irine Ronin and Nathalie Q Balaban

    Citation: Genome Medicine 2014 6:112

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  6. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Medicine 2014 6:111

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  7. Content type: Review

    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...

    Authors: Elizabeth A Winzeler and Micah J Manary

    Citation: Genome Biology 2014 15:544

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  8. Content type: Research

    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...

    Authors: 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

    Citation: Genome Biology 2014 15:540

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  9. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Biology 2014 15:510

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  10. Content type: Software

    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...

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

    Citation: Genome Medicine 2014 6:90

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  11. Content type: Research

    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...

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

    Citation: Genome Medicine 2014 6:70

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  12. Content type: Software

    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...

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

    Citation: Genome Medicine 2014 6:100

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  13. Content type: Research

    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...

    Authors: 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

    Citation: Genome Medicine 2014 6:541

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  14. Content type: Research highlight

    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...

    Authors: Patrick Tang and Jennifer L Gardy

    Citation: Genome Medicine 2014 6:104

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  15. Content type: Method

    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...

    Authors: 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

    Citation: Genome Biology 2014 15:517

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  16. Content type: Software

    Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequence...

    Authors: Todd J Treangen, Brian D Ondov, Sergey Koren and Adam M Phillippy

    Citation: Genome Biology 2014 15:524

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  17. Content type: Opinion

    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...

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

    Citation: Genome Medicine 2014 6:106

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  18. Content type: Method

    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...

    Authors: 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…

    Citation: Genome Biology 2014 15:519

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  19. Content type: Method

    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 ...

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

    Citation: Genome Medicine 2014 6:101

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  20. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Biology 2014 15:532

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  21. Content type: Review

    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...

    Authors: Paolo Gabrieli, Andrea Smidler and Flaminia Catteruccia

    Citation: Genome Biology 2014 15:535

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  22. Content type: Research

    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...

    Authors: 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

    Citation: Genome Medicine 2014 6:99

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  23. Content type: Research

    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...

    Authors: 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

    Citation: Genome Biology 2014 15:511

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  24. Content type: Research highlight

    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.

    Authors: Anastasia Koch and Robert John Wilkinson

    Citation: Genome Biology 2014 15:520

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  25. Content type: Research highlight

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

    Authors: Chase L Beisel, Ahmed A Gomaa and Rodolphe Barrangou

    Citation: Genome Biology 2014 15:516

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  26. Content type: Research

    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...

    Authors: 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

    Citation: Genome Biology 2014 15:490

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  27. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Biology 2014 15:478

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  28. Content type: Comment

    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...

    Authors: Onikepe A Folarin, Anise N Happi and Christian T Happi

    Citation: Genome Biology 2014 15:515

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  29. Content type: Research

    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...

    Authors: 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…

    Citation: Genome Biology 2014 15:505

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  30. Content type: Research

    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...

    Authors: 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

    Citation: Genome Biology 2014 15:502

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  31. Content type: Research

    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...

    Authors: 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

    Citation: Genome Biology 2014 15:504

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  32. Content type: Research

    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...

    Authors: 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

    Citation: Genome Biology 2014 15:493

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