Genomics|Update|Infectious Diseases ► Advanced Molecular Detection in Action

Genomics|Update|Infectious Diseases

Volume 34  Number 13  April 2-9, 2015

Advanced Molecular Detection in Action

• Antimicrobials, Vaccines, Interventions
• Detection & Diagnosis
• Epidemiology, Outbreaks, Transmission
• Evolution, Ecology, Pathogenicity, Populations

• Host-Pathogen Interactions
• Methods
• Policy
• Reviews, News & Commentaries

Antimicrobials, Vaccines, Interventions

KPC and NDM-1 are harbored by related Enterobacteriaceae strains and plasmid backbones form distinct geographies. 
Pesesky MW, et al. Emerging Infectious Diseases, Jun 2015.

Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference. 
Shen SH et al. Proc. Natl. Acad. Sci. U.S.A. 2015 Mar 30.

InSilixa awarded NIH grant to develop point-of-care test for drug-resistant tuberculosisGenomeWeb, Apr 1, 2015.

Collateral sensitivity of antibiotic-resistant microbes. 
Pál Csaba et al. Trends Microbiol. 2015 Mar 25.

Molecular assessment of artemisinin resistance markers, polymorphisms in the k13 propeller, and a multidrug-resistance gene in the eastern and western border areas of Myanmar. 
Nyunt M et al. Clin. Infect. Dis. 2015 Apr 15. (8) 1208-15

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Detection and Diagnosis

An evaluation of the level of agreement in Bordetella species identification in three United States laboratories during a period of increased pertussis. 
Burgos-Rivera B et al. J. Clin. Microbiol. 2015 Mar 25. (CDC Author)

Comparison of species identification of endocarditis associated viridans streptococci using rnpB genotyping and 2 MALDI-TOF systems. 
Isaksson J et al. Diagn. Microbiol. Infect. Dis. 2015 Apr (4) 240-5

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Epidemiology, Outbreaks, Transmission

A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012?14): a retrospective cohort study 
Greninger AL, et al. Lancet Infect Dis, Mar 31, 2015.

Tracking a tuberculosis outbreak over 21 years: strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing. 
Stucki D et al. J. Infect. Dis. 2015 Apr 15. (8) 1306-16

Dynamics of MDR Enterobacter cloacae outbreaks in a neonatal unit in Nepal: insights using wider sampling frames and next-generation sequencing. 
Stoesser N et al. J. Antimicrob. Chemother. 2015 Apr (4) 1008-15

Clonal outbreak of Plasmodium falciparum infection in Eastern Panama. 
Obaldia N et al. J. Infect. Dis. 2015 Apr 1. (7) 1087-96

Outbreak of severe zoonotic vaccinia virus infection, Southeastern Brazil. 
Abrahão J S et al. Emerging Infect. Dis. 2015 Apr (4) 695-698

Endoscopic Retrograde Cholangiopancreatography-Associated AmpC Escherichia coli Outbreak.
Wendorf KA et al. Infect Control Hosp Epidemiol 2015 Mar 30. 1-9

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Evolution, Ecology, Pathogenicity, Populations

Mutation rate and genotype variation of Ebola virus from Mali case sequences 
Hoenen T, et al. Science, Mar 26, 2015.

Compartmentalized replication of R5 T cell-tropic HIV-1 in the central nervous system early in the course of infection. 
Sturdevant CB et al. PLoS Pathog. 2015 Mar (3) e1004720

Selective and genetic constraints on pneumococcal serotype switching. 
Croucher NJ et al. PLoS Genet. 2015 Mar (3) e1005095

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. 
Weinert LA et al. Nat Commun 2015 6740

Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission. 
Paterson GK et al. Nat Commun 2015 6560

Comparison of whole genome sequences from human and non-human Escherichia coli O26 strains. 
Norman KN et al. Front Cell Infect Microbiol 2015 21

Multiple-locus variable-number tandem-repeat analysis of Francisella tularensis from Quebec, Canada. 
Antonation KS et al. Lett. Appl. Microbiol. 2015 Apr (4) 328-33

Population structure and antimicrobial resistance of invasive serotype IV group B streptococcus, Toronto, Ontario, Canada. 
Teatero S et al. Emerging Infect. Dis. 2015 Apr (4) 585-591

Sequence variability and geographic distribution of lassa virus, Sierra Leone. 
Leski TA et al. Emerging Infect. Dis. 2015 Apr (4) 609-618

Co-infection with avian (H7N9) and pandemic (H1N1) 2009 influenza viruses, China. 
Zhang W et al. Emerging Infect. Dis. 2015 Apr (4) 715-718

Bat coronavirus in Brazil related to Appalachian ridge and porcine epidemic diarrhea viruses. 
Simas Paulo VM et al. Emerging Infect. Dis. 2015 Apr (4) 729-731

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Host-Pathogen Interactions

Life-threatening influenza and impaired interferon amplification in human IRF7 deficiency 
Ciancanelli MJ, et al. Science, Mar 26, 2015.

Cytomegalovirus infection enhances the immune response to influenza
Furman D, et al. Sci Transl Med 2015;7(281):281ra43

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Methods

MAFCO: A compression tool for MAF files 
Matos LM, et al. PLoS Genetics, Mar 27, 2015.

Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer. 
Kilianski A et al. Gigascience 2015 12

A game theoretic framework for analyzing re-identification risk. 
Wan Z et al. PLoS ONE 2015 (3) e0120592

Virus-like particle system identifies the endonuclease domain of Crimean-Congo hemorrhagic fever virus. 
Devignot S et al. J. Virol. 2015 Mar 25.

Global avian influenza surveillance in wild birds: A strategy to capture viral diversity. 
Machalaba CC et al. Emerging Infect. Dis. 2015 Apr (4)

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Policy

A consensus development conference model for establishing health policy for surveillance and screening of antimicrobial-resistant organisms. 
Buick S et al. Clin. Infect. Dis. 2015 Apr 1. (7) 1095-101

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Reviews, News and Commentaries

Enzyme improves CRISPR, by Grens K. The Scientist, Apr 1, 2015.

Smartphone HIV test, 
Nature Biotechnology 2015;33:221

Obama Seeks to Double Funding to Fight Antibiotic Resistance, Tavernise S, Shear MD. New York Times, Mar 27, 2015.

Liberia Recommends Ebola Survivors Practice Safe Sex Indefinitely, Fink S. New York Times, Mar 28, 2015.

Ebola's fast evolution questioned, 
Callaway E. Nature, Mar 26, 2015.

Genome Canada launches C$30.5M genomics innovation network, GenomeWeb, Mar 31, 2015

Outbreak of EV-D68 detected by cross-reactivity in GenMark respiratory viral panel Johnson M. GenomeWeb, Mar 31, 2015.

Enterovirus 68 may be linked to paralysis in children, study says Saint Louis C. New York Times, Mar 31, 2015.

Researchers demonstrate amplicon sequencing on MinIon with eye toward point-of-care applications Heger M, Genome Web, Mar 26, 2015.

MeMed rolling out proteomic test to distinguish between bacterial, viral infections Bonislawski A. GenomeWeb, Mar 27, 2015.

Catalog of earth microbes could help find alien life Cofield C. Yahoo News, Apr 1, 2015.

Speeding new antibiotics to market: a fake fix? 
Doshi Peter et al. BMJ 2015 h1453

Viral cell-to-cell transmission-why less is more. 
Richardson Lauren A et al. PLoS Biol. 2015 Mar (3) e1002095

Successful test launch for nanopore sequencing. 
Loman Nicholas J et al. Nat. Methods 2015 Mar 31. (4) 303-304

A microbiological revolution meets an ancient disease: improving the management of tuberculosis with genomics. 
Wlodarska Marta et al. Clin. Microbiol. Rev. 2015 Apr (2) 523-539

Developing vaccines for an aging population
Black S, et al. Sci Transl Med 2015;7(281):281ps8