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

Genomics|Update|Infectious Diseases

Volume 34  Number 5  February 5-12, 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

Novel gentamicin resistance genes in Campylobacter isolated from humans and retail meats in the USA 
Zhao S, et al. J Antimicrob Chemother. 2015 Feb 1. pii: dkv001. [Epub ahead of print]

Persistence of Neisseria gonorrhoeae DNA following treatment for pharyngeal and rectal gonorrhea is influenced by antibiotic susceptibility and reinfection
Bissessor M, et al. Clin Infect Dis 2015; 60(4):  557-563.

Comment:
Persistent gonococcal DNA: Artifact or real? further insights into the biology of a remarkable pathogen.
Zenilman JM. Clin Infect Dis. 2015 Feb 15;60(4):564-5.

Evolution of carbapenem-resistant Acinetobacter baumannii revealed through whole-genome sequencing and comparative genomic analysis
Li H, et al. Antimicrob Agents Chemother 2015; 59(2): 1168-1176.

Genomic insights into intrinsic and acquired drug resistance mechanisms in Achromobacter xylosoxidans
Hu Y, et al. Antimicrob Agents Chemother 2015; 59(2): 1152-1161.

Evolution and transmission patterns of extensively drug-resistant tuberculosis in China 
Wang F, et al. Antimicrob Agents Chemother 2015; 59(2): 818-825.

Macrolide-resistant Mycoplasma pneumoniae in adults in Zhejiang, China 
Zhou Z, et al. Antimicrob Agents Chemother 2015; 59(2): 1048-1051.

Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial 
Edlefsen PT, et al. PLoS Comput Biol. 2015 Feb 3;11(2):e1003973.

Molecular mechanisms of fluconazole resistance in Candida parapsilosis isolates from a U.S. surveillance system
Grossman NT, et al. Antimicrob Agents Chemother 2015; 59(2): 1030-1037.

Population genetics of Trypanosoma brucei gambiense in sleeping sickness patients with treatment failures in the focus of Mbuji-Mayi, Democratic Republic of the Congo
Pyana PP, et al. Infect Genet Evol 2015; 30: 128–133.

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Detection and Diagnosis

Sepsis pathogen identification 
Chun K, et al. J Lab Autom. 2015 Jan 28.

A systematic review of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry compared to routine microbiological methods for the time taken to identify microbial organisms from positive blood cultures. 
Dixon P, et al. Eur J Clin Microbiol Infect Dis. 2015 Jan 27.

Transcriptional profiling is superior to procalcitonin to discriminate bacterial vs viral lower respiratory tract infections in hospitalized adults. 
Suarez NM, et al. J Infect Dis. 2015 Jan 29.

Comment:
Moving towards prime time: host signatures for diagnosis of respiratory infections.
Tsalik E, et al. J Infect Dis. 2015 Jan 29.

Isolation and development of bioluminescent reporter phages for bacterial dysentery. 
Schofield DA, et al. Eur J Clin Microbiol Infect Dis. 2015 Feb;34(2):395-403.

Genome sequence of enterovirus d68 and clinical disease, Thailand.
Vongpunsawad S, et al. Emerg Infect Dis. 2015 Feb;21(2):384.

Differentiation of acute from chronic hepatitis C virus infection by NS5B deep sequencing: A population-level tool for incidence estimation.
Montoya V, et al. Hepatology. 2015 Feb 2.

A smartphone dongle for diagnosis of infectious diseases at the point of care
Laksanasopin T, et al. Sci Transl Med 2015; 7(273): 273re1. 

Successful detection and genotyping of rubella virus from preserved umbilical cord of patients with congenital rubella syndrome. 
Miyata I, et al. Clin Infect Dis. 2015 Feb 15;60(4):605-7.

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Epidemiology, Outbreaks, Transmission

Comparative whole genome sequencing of community-associated methicillin-resistant Staphylococcus aureus sequence type 8 from primary care clinics in a Texas community
Lee GC, et al. Pharmacotherapy. 2015 Feb 3.

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Evolution, Ecology, Pathogenicity, Populations

Increase in endemic Neisseria meningitidis capsular group W sequence type 11 complex associated with severe invasive disease in England and Wales
Ladhani SN, et al. Clin Infect Dis. 2015 Feb 15;60(4):578-85.

Novel reassortant highly pathogenic H5N6 avian influenza viruses in poultry in China 
Wu H, et al. Infect Genet Evol, Jan 31, 2015.

Emergence of a new lineage of dengue virus type 2 identified in travelers entering Western Australia from Indonesia, 2010-2012
Ernst T, et al. PLoS Negl Trop Dis 9(1): e0003442.

Population structure of the Chagas disease vector Triatoma infestans in an urban environment
Khatchikian CE, et al. PLoS Negl Trop Dis 9(2): e0003425.

Classification of Bartonella strains associated with straw-colored fruit bats (Eidolon helvum) across Africa using a multi-locus sequence typing platform
Bai Y, et al. PLoS Negl Trop Dis. 2015 Jan 30;9(1):e0003478.

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Host-Pathogen Interactions

Discovery of six new susceptibility loci and analysis of pleiotropic effects in leprosy 
Liu H. Nat Genet, Feb 2, 2015.  PMID: 25642632

IL-18 is associated with protection against rhinovirus-induced colds and asthma exacerbations.
Jackson DJ, et al. Clin Infect Dis. 2015 Feb 2.

Mitochondrial DNA stress primes the antiviral innate immune response 
West AP, et al. Nature, Feb 2, 2015. PMID: 25642965

Extensive strain-level copy-number variation across human gut microbiome species
Greenblum S, et al. Cell, Jan 28, 2015.

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Methods

RNA-Rocket: An RNA-seq analysis resource for infectious disease research
Warren AS, et al. Bioinformatics, Jan 7, 2015.

Comment:
VBI-led team introduces infectious disease-focused resource for analyzing RNA-seq data
Anderson A. Feb 3, 2015.

Innovative techniques, sensors, and approaches for imaging biofilms at different scales
Neu TR, Lawrence JR.  Trends Microbiol , Jan 23, 2015.

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Policy

The collection, linking and use of data in biomedical research and health care: ethical issues 
Nuffield Council on Bioethics (UK), Feb 2015. 

Comment:
Let public have greater say over big health data 
Richards M. New Scientist, Feb 3, 2015.

Tougher penalties, including imprisonment, are urged for misuse of personal data
Hawkes N. BMJ 2015;350:h619.

Balancing privacy versus accuracy in research protocols
Goroff DL. Science 2015; 347: 479-480.  

Control use of data to protect privacy
Landau S. Science 2015; 347: 504-506.

Risk of exposure
Enserink M. Science 2015; 347: 498-500.

Public perceptions of bacterial whole-genome sequencing for tuberculosis
Davies A, et al. Trends Genet 2015 Feb;31(2):58-60.

A new initiative on precision medicine
Collins FS, Varmus H. New Engl J Med, Jan 30, 2015.

Centennial Shigella
Akst J. The Scientist, Feb 1, 2015.

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Reviews, News and Commentaries

Predictions for the field of infectious diseases for 2015
Bartlett J. Medscape Infect Dis, Jan 29, 2015. (registration)

Obama budget seeks big boost for science
Deng B, et al. Nature, Feb 3, 2015.

A new beginning for semiconductor sequencing
Krol A. Bio-IT World, Feb 2, 2015.

Ebola drug trial canceled
Akst J. The Scientist, Feb 2, 2015.

People identified through credit-card use alone
Deng B, et al. Nature, Jan 29, 2015.

NIH commits $8M for systems biology studies of antibacterial resistance
GenomeWeb, Feb 2, 2015.

Tetracore wins NIH funds for chikungunya/dengue MDx on its POC thermocycler 
Johnson M. GenomeWeb, Jan 30, 2015.

IBM, Mars collaborate on genomics to improve food safety
GenomeWeb, Jan 30, 2015.

GenomeWeb updates on molecular diagnostics:
Formerly Twistnostics, Scanogen looks to commercialize first MDx test for TB