BioMed Central | Article collections | Genomics of infectious diseases special issue

BioMed Central | Article collections | Genomics of infectious diseases special issue

Genome Medicine: Genomics of infectious diseases special issue, Nov 2014

Genomics of infectious diseases special issue

Infectious diseases are major contributors to global morbidity and mortality, and have a devastating impact on public health. The World Health Organization estimates that 1 in 3 deaths worldwide are due to an infectious disease, with a disproportionate number occurring in developing regions.

While the completion of the first genome sequence of a pathogen, Haemophilus influenzae, in 1995 took decades of work, in recent years, high-throughput technologies have revolutionized the study of pathogens. 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.

In this cross-journal special issue, guest edited by George Weinstock (The Jackson Laboratory for Genomic Medicine, USA) andSharon Peacock (University of Cambridge, UK), Genome Biology and Genome Medicine take stock of where we are now, with a collection of primary research and commissioned 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.

Collection published: 3 November 2014

Last updated: 28 November 2014

	Research    Next generation sequencing analysis of nine Corynebacterium ulcerans isolates reveals zoonotic transmission and a novel putative diphtheria toxin encoding pathogenicity island Dominik M Meinel, Gabriele Margos, Regina Konrad, Stefan Krebs, Helmut Blum, Andreas SingGenome Medicine 2014, 6:113 (28 November 2014) Abstract | Provisional PDF| Editor’s summary
	Method    Systematic identification and quantification of phase variation in commensal and pathogenic Escherichia coli Amir Goldberg, Ofer Fridman, Irine Ronin, Nathalie Q BalabanGenome Medicine 2014, 6:112 (28 November 2014) Abstract | Provisional PDF| Editor’s summary
	Research    An integrated transcriptome and expressed variant analysis of sepsis survival and death 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, G Corey, Geoffrey S Ginsburg, Charles B Cairns, Ronny M Otero, Vance G Fowler, Emanuel P Rivers, Christopher W Woods, Stephen F KingsmoreGenome Medicine 2014, 6:111 (26 November 2014) Abstract | Provisional PDF| Editor’s summary
	Review    Drug resistance genomics of the antimalarial drug artemisinin Elizabeth A Winzeler, Micah J ManaryGenome Biology 2014, 15:544 (25 November 2014) Abstract | Full text | PDF| Editor’s summary
	Research    Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity. Stuart D Dowall, David A Matthews, Isabel Garcia-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, Julian A HiscoxGenome Biology 2014, 15:540 (22 November 2014) Abstract | Provisional PDF | PubMed| Editor’s summary
	Editorial    Human infectious diseases in the genomics era: where do we go from here? Ripudaman K BainsGenome Biology 2014, 15:529 (22 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Review    Genomic analysis of emerging pathogens: methods, application and future trends Lucy M Li, Nicholas C Grassly, Christophe FraserGenome Biology 2014, 15:541 (22 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Review    Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology Timothy D Read, Ruth C MasseyGenome Medicine 2014, 6:109 (22 November 2014) Abstract | Full text | PDF| Editor’s summary
	Research    The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion Hayley M Bennett, Hoi Ping Mok, Effrossyni Gkrania-Klotsas, Eleanor J Stanley, Isheng J Tsai, Nagui M Antoun, Avril Coghlan, Bhavana Harsha, Alessandra Traini, Diogo M Ribeiro, Sascha Steinbass, Sebastian B Lucas, Kieren S.J Allinson, Stephen J Price, Thomas S Santarius, Andrew J Carmichael, Peter L Chiodini, Nancy Holroyd, Andrew F Dean, Matthew BerrimanGenome Biology 2014, 15:510 (21 November 2014) Abstract | Provisional PDF| Editor’s summary
	Research highlight    Stopping outbreaks with real-time genomic epidemiology Patrick Tang, Jennifer L GardyGenome Medicine 2014, 6:104 (20 November 2014) Abstract | Full text | PDF| Editor’s summary
	Research    Global gene expression profiling identifies new therapeutic targets in acute KD Long T Hoang, Chisato Shimizu, Ling Ling, Nazri M Naim, Chuen C Khorr, Adriana H Tremoulet, Victoria Wright, Michael Levin, Martin L Hibberd, Jane C BurnsGenome Medicine 2014, 6:102 (20 November 2014) Abstract | Provisional PDF| Editor’s summary
	Software    YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens Darren Abbey, Jason Funt, Mor N Lurie-Weinberger, Dawn A Thompson, Aviv Regev, Chad L Myers, Judith BermanGenome Medicine 2014, 6:100 (20 November 2014) Abstract | Provisional PDF| Editor’s summary
	Comment    Single cell genomics of bacterial pathogens: outlook for infectious disease research Jeffrey S McLean, Roger S LaskenGenome Medicine 2014, 6:108 (20 November 2014) Abstract | Full text | PDF| Editor’s summary
	Software    SRST2: Rapid genomic surveillance for public health and hospital microbiology labs Michael Inouye, Harriet Dashnow, Lesley-Ann Raven, Mark B Schultz, Bernard J Pope, Takehiro Tomita, Justin Zobel, Kathryn E HoltGenome Medicine 2014, 6:90 (20 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Research    Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England Mihail R Halachev, Jacqueline Chan, Chrystala I Constantinidou, Nicola Cumley, Craig Bradley, Matthew Smith-Banks, Beryl Oppenheim, Mark J PallenGenome Medicine 2014, 6:70 (20 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Editorial    Next-generation pathogen genomics George M Weinstock, Sharon J PeacockGenome Biology 2014, 15:528 (19 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Software    Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes Todd J Treangen, Brian D Ondov, Sergey Koren, Adam M PhillippyGenome Biology 2014, 15:524 (19 November 2014) Abstract | Provisional PDF| Editor’s summary
	Method    BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads Lewis Z Hong, Shuzhen Hong, Han Teng Wong, Pauline PK Aw, Cheng Yan, Andreas Wilm, Paola F de Sessions, Seng Gee Lim, Niranjan Nagarajan, Martin L Hibberd, Stephen R Quake, William F BurkholderGenome Biology 2014, 15:517 (19 November 2014) Abstract | Provisional PDF| Editor’s summary
	Editorial    Microbial sequencing to improve individual and population health Sharon J Peacock, George M WeinstockGenome Medicine 2014, 6:103 (19 November 2014) Abstract | Full text | PDF| Editor’s summary
	Opinion    Genomics and infectious disease: a call to identify the ethical, legal and social implications for public health and clinical practice Gail Geller, Rachel Dvoskin, Chloe L Thio, Priya Duggal, Michelle H Lewis, Theodore C Bailey, Andrea Sutherland, Daniel A Salmon, Jeffrey P KahnGenome Medicine 2014, 6:106 (18 November 2014) Abstract | Full text | PDF| Editor’s summary
	Review    Epidemiologic data and pathogen genome sequences: a powerful synergy for public health Yonatan H Grad, Marc LipsitchGenome Biology 2014, 15:538 (18 November 2014) Abstract | Full text | PDF| Editor’s summary
	Method    Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses in clinical and biological samples 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, Ikponmwosa Odia, Philomena E Ehiane, Onikepe Folarin, Augustine Goba, S.Humarr Khan, Donald S Grant, Anna Honko, Lisa Hensley, Christian Happi, Robert F Garry, Christine M Malboeuf, Bruce W Birren, Andreas Gnirke, Joshua Z Levin, Pardis C SabetiGenome Biology 2014, 15:519 (18 November 2014) Abstract | Provisional PDF | PubMed| Editor’s summary
	Research    The conjunctival microbiome in health and trachomatous disease: a case control study Yanjiao Zhou, Martin J Holland, Pateh Makalo, Hassan Joof, Chrissy h Roberts, David Mabey, Robin L Bailey, Matthew J Burton, George M Weinstock, Sarah E BurrGenome Medicine 2014, 6:99 (15 November 2014) Abstract | Provisional PDF| Editor’s summary
	Research    Proteomics informed by transcriptomics reveals Hendra virus sensitizes bat cells to TRAIL mediated apoptosis 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, David Matthews, Lin-Fa WangGenome Biology 2014, 15:532 (15 November 2014) Abstract | Provisional PDF | PubMed| Editor’s summary
	Method    A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens Maha R Farhat, B Shapiro, Samuel K Sheppard, Caroline Colijn, Megan MurrayGenome Medicine 2014, 6:101 (15 November 2014) Abstract | Provisional PDF| Editor’s summary
	Review    Engineering the control of mosquito-borne infectious diseases Paolo Gabrieli, Andrea Smidler, Flaminia CatterucciaGenome Biology 2014, 15:535 (15 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Research     A Genomic and Evolutionary Approach Reveals Non-Genetic Drug Resistance in Malaria Jonathan D Herman, Daniel P Rice, Ulf Ribacke, Jacob Silterra, Amy A Deik, Eli Moss, Kate M Broadbent, Daniel E Neafsey, Michael M Desai, Clary B Clish, Ralph Mazitschek, Dyann F WirthGenome Biology 2014, 15:511 (14 November 2014) Abstract | Provisional PDF| Editor’s summary
	Research highlight    The road to drug resistance in Mycobacterium tuberculosis Anastasia Koch, Robert WilkinsonGenome Biology 2014, 15:520 (13 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Research highlight    A CRISPR design for next-generation antimicrobials Chase L Beisel, Ahmed A Gomaa, Rodolphe BarrangouGenome Biology 2014, 15:516 (8 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Research     Evolution of extensively drug-resistant Mycobacterium tuberculosis from a susceptible ancestor in a single patient Vegard Eldholm, Gunnstein Norheim, Bent von der Lippe, Wibeke Kinander, Ulf R Dahle, Dominique A Caugant, Turid Mannsåker, Anne Mengshoel, Anne Dyrhol-Riise, Francois BallouxGenome Biology 2014, 15:490 (7 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Comment     Empowering African genomics for infectious disease control Onikepe A Folarin, Anise N Happi, Christian T HappiGenome Biology 2014, 15:515 (7 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Research highlight    Bringing non-human primate research into the post-genomic era: how monkeys are teaching us about elite controllers of HIV/AIDS Eric J VallenderGenome Biology 2014, 15:507 (7 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Review    Translating genomics research into control of tuberculosis: lessons learned and future prospects Digby F Warner, Valerie MizrahiGenome Biology 2014, 15:514 (7 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Research    Whole genome sequencing of SIV-infected macaques identifies candidate loci that may contribute to host control of virus replication Adam J Ericsen, Gabriel J Starrett, Justin M Greene, Michael Lauck, Muthuswamy Raveendran, David 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, Thomas C Friedrich, Jeffrey Rogers, David H O’ConnorGenome Biology 2014, 15:478 (7 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Research    Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' Disease 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, Gernot Glöckner, Elizabeth L Hartland, Carmen BuchrieserGenome Biology 2014, 15:505 (3 November 2014) Abstract | Provisional PDF| Editor’s summary
	Research    Genome-wide RIP-Chip analysis of translational repressor-bound mRNAs in the Plasmodium gametocyte Ana Guerreiro, Elena Deligianni, Jorge M Santos, Patricia Silva, Christos Louis, Arnab Pain, Chris J Janse, Blandine Franke-Fayard, Celine K Carret, Inga Siden-Kiamos, Gunnar R MairGenome Biology 2014, 15:493 (3 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Research     Staphylococcus aureus gene expression in a rat model of infective endocarditis Frank Hanses, Christelle Roux, Paul M Dunman, Bernd Salzberger, Jean C LeeGenome Medicine 2014, 6:93 (3 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Research     Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires' disease outbreak Paul McAdam, Charles vander broek, Diane Lindsay, Melissa Ward, Mary Hanson, Michael Gillies, Mike Watson, Joanne Stevens, Giles Edwards, Ross FitzgeraldGenome Biology 2014, 15:504 (3 November 2014) Abstract | Provisional PDF | PubMed| Editor’s summary
	Research     Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network Tige R Rustad, Kyle J Minch, Shuyi Ma, Jessica K Winkler, Samuel Hobbes, Mark J Hickey, William Brabant, Serdar Turkarslan, Nathan D Price, Nitin S Baliga, David R ShermanGenome Biology 2014, 15:502 (3 November 2014) Abstract | Provisional PDF | PubMed| Editor’s summary