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

Genomics|Update|Infectious Diseases

Volume 35  Number 1  July 2-9, 2015

Advanced Molecular Detection in Action

• Antimicrobials/ Vaccines/ Interventions
• Detection/ Diagnosis
• Epidemiology/ Outbreaks/ Transmission
• Evolution/ Ecology/ Populations

• Host-Microbe Interactions
• Methods/ Tools
• Pathogenicity / Antimicrobial Resistance
• Reviews/ News/ Commentaries

Antimicrobials/ Vaccines/ Interventions

Update on vaccine-derived polioviruses - worldwide, January 2014-March 2015.
Diop OM et al. MMWR Morb. Mortal. Wkly. Rep. 2015 Jun 19. (23) 640-6 (CDC Author)

Machine learning models and pathway genome data base for Trypanosoma cruzi drug discovery.
Ekins S et al. PLoS Negl Trop Dis 2015 Jun (6) e0003878

Genomic analysis of isolates from the United Kingdom 2012 pertussis outbreak reveals that vaccine antigen genes are unusually fast evolving.
Sealey KL et al. J. Infect. Dis. 2015 Jul 15. (2) 294-301

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Detection/ Diagnosis

Acute flaccid paralysis associated with novel enterovirus C105
Horner LM, et al. Emerg Infect Dis, Oct 2015.

Aspergillus PCR: a systematic review of evidence for clinical use in comparison with antigen testing
White PL, et al. Clin Infect Dis, Jun 25, 2015.

Naturally occurring hepatitis B virus surface antigen mutant variants in Malaysian blood donors and vaccinees.
Hudu SA et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Jul (7) 1349-59

ReEBOV antigen rapid test kit for point-of-care and laboratory-based testing for Ebola virus disease: a field validation study.
Broadhurst MJ et al. Lancet 2015 Jun 25.

Specificity and strain-typing capabilities of nanorod array-surface enhanced raman spectroscopy for mycoplasma pneumoniae detection.
Henderson KC et al. PLoS ONE 2015 (6) e0131831 (CDC Author)

Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage.
Phan TG et al. Virology 2015 Aug 98-104

The discovery, function and development of the variable number tandem repeats in different Mycobacterium species.
Sun Z et al. Crit. Rev. Microbiol. 2015 Jun 19. 1-21

Superiority of transcriptional profiling over procalcitonin for distinguishing bacterial from viral lower respiratory tract infections in hospitalized adults.
Suarez NM et al. J. Infect. Dis. 2015 Jul 15. (2) 213-22

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Epidemiology/ Outbreaks/ Transmission

Zika virus outbreak, Bahia, Brazil [letter]. 
Campos GS, Bandeira AC, Sardi SI. Emerg Infect Dis, Oct 2015.

Targeting prevention based on molecular epidemiology among deeply sampled sub-networks of men have who sex with men
Wang X, et al. Clin Infect Dis, Jun 30, 2015.

Sequence types of Staphylococcus epidermidis associated with prosthetic joint infections are not present in the laminar airflow during prosthetic joint surgery.
Månsson E et al. APMIS 2015 Jul (7) 589-95

Pneumonia outbreak caused by Chlamydophila pneumoniae among US Air Force Academy cadets, Colorado, USA.
Fajardo KA et al. Emerging Infect. Dis. 2015 Jun (6) 1049-51

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Evolution/ Ecology/ Populations

Novel arenavirus isolates from Namaqua rock mice, Namibia, Southern Africa. 
Witkowski PT, Kallies R, Hoveka J, Auste B, Ithete NL, Soltys T, et al. Emerg Infect Dis, Jul 2015.

Distinct lineages of bufavirus in wild shrews and nonhuman primates. 
Sasaki M, Orba Y, Anindita PD, Ishii A, Ueno K, Hang'ombe BM, et al. Emerg Infect Dis, Jul 2015.

Characterization of 3 megabase-sized circular replicons from Vibrio cholerae [letter]. 
Okada K, Natakuathung W, Na-Ubol M, Roobthaisong A, Wongboot W, Maruyama F, et al. Emerg Infect Dis, Jul 2015.

Diversity of Bartonella spp. in bats, southern Vietnam [letter].
Anh PH, Van Cuong N, Son NT, Tue NT, Kosoy M, Woolhouse MEJ, et al. Emerg Infect Dis, Jul 2015. (CDC Author)

Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions.
Anstead CA et al. Nat Commun 2015 7344

Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum.
Isakov O et al. Bioinformatics 2015 Jul 1. (13) 2141-50

Phylodynamics of Enterovirus A71-associated hand, foot and mouth disease in Viet Nam.
Geoghegan JL et al. J. Virol. 2015 Jun 17. (CDC Author)

Filovirus RNA in fruit bats, China [letter]. 
He B, Feng Y, Zhang H, Xu Lin, Yang W, Zhang Y, et al. Emerg Infect Dis. 2015 Sep [date cited].

Phylogenetic analysis of Bunyamwera and Ngari viruses (family Bunyaviridae, genus Orthobunyavirus) isolated in Kenya.
Odhiambo C et al. Epidemiol. Infect. 2015 Jun 29. 1-7

A novel recombinant lineage's contribution to the outbreak of coxsackievirus A6-associated hand, foot and mouth disease in Shanghai, China, 2012-2013.
Feng X et al. Sci Rep 2015 11700

Full-genome sequencing as a basis for molecular epidemiology studies of bluetongue Virus in India.
Maan S et al. PLoS ONE 2015 (6) e0131257

Phylodynamics of H5N1 highly pathogenic avian influenza in Europe, 2005-2010: Potential for molecular surveillance of new outbreaks.
Alkhamis MA et al. Viruses 2015 (6) 3310-28

The mitochondrial genome of a Texas outbreak strain of the cattle tick, Rhipicephalus (Boophilus) microplus, derived from whole genome sequencing Pacific Biosciences and Illumina reads.
McCooke JK et al. Gene 2015 Jun 25.

Bacteriophages isolated from chicken meat and the horizontal transfer of antimicrobial resistance genes.
Shousha A et al. Appl. Environ. Microbiol. 2015 Jul 15. (14) 4600-6

Recombination analysis of herpes simplex virus 1 reveals a bias toward GC content and the inverted repeat regions.
Lee K et al. J. Virol. 2015 Jul 15. (14) 7214-23

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Host-Microbe Interactions

Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis
Kang D, et al. Science Transl Med, Jun 24, 2015.

Detection of somatic mutations and HPV in the saliva and plasma of patients with head and neck squamous cell carcinomas
Wang Y, et al. Sci Transl Med, Jun 24, 2015.

Association of the functional MICA-129 polymorphism with the severity of chronic Chagas heart disease
Ayo CM, et al. Clin Infect Dis, Jun 30, 2015.

Polymorphisms in the TOLLIP gene influence susceptibility to cutaneous leishmaniasis caused by leishmania guyanensis in the Amazonas state of Brazil.
Araujo FJ de et al. PLoS Negl Trop Dis 2015 Jun (6) e0003875

Global mapping of the Inc-human interactome reveals that retromer restricts chlamydia infection.
Mirrashidi KM et al. Cell Host Microbe 2015 Jun 24.

Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial 
Moayyedi P, et al. Gastroenterol Jul 2015; 149(1): 102-109.

Differences in gut microbiota between atopic and healthy children.
Drell T et al. Curr. Microbiol. 2015 Aug (2) 177-83

Varicella zoster virus in temporal arteries of patients with giant cell arteritis.
Gilden D et al. J. Infect. Dis. 2015 Jul 15. S37-9

Antibodies to influenza nucleoprotein cross-react with human hypocretin receptor 2
Ahmed SS, et al. Sci Transl Med, Jul 1, 2015.

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Methods/Tools

Unified representation of genetic variants.
Tan A et al. Bioinformatics 2015 Jul 1. (13) 2202-4

EpiToolKit-a web-based workbench for vaccine design.
Schubert B et al. Bioinformatics 2015 Jul 1. (13) 2211-3

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.
Giraldo-Calderón GI et al. Nucleic Acids Res. 2015 Jan (Database issue) D707-13

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice.
Walker AW et al. Microbiome 2015 26

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Pathogenicity / Antimicrobial Resistance

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.
Walker TM et al. Lancet Infect Dis 2015 Jun 23.

Genome analysis of the first extensively drug-resistant (XDR) mycobacterium tuberculosis in Malaysia provides insights into the genetic basis of its biology and drug resistance.
Kuan CS et al. PLoS ONE 2015 (6) e0131694

Genotypic diversity is associated with clinical outcome and phenotype in cryptococcal meningitis across Southern Africa.
Beale MA et al. PLoS Negl Trop Dis 2015 Jun (6) e0003847

Early emergence of Yersinia pestis as a severe respiratory pathogen
Zimbler DL, et al. Nat Comm, Jun 30, 2015.

Bacteriophages isolated from chicken meat and the horizontal transfer of antimicrobial resistance genes.
Shousha A et al. Appl. Environ. Microbiol. 2015 Jul 15. (14) 4600-6

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Reviews/ News/ Commentaries

Noblis Readies Internal Pathogen Identification Software for Commercialization
Thomas UG. GenomeWeb, Jun 26, 2015.

Nearly instantaneous, finger-prick test for Ebola could be game changer
Cha AE. Washington Post, Jun 26, 2015.

Ceres Receives $746K from Gates Foundation for TB Test Development
GenomeWeb, Jun 30, 2015.

A New Device Could Diagnose Malaria in a Matter of Minutes
Kaufmann E. mic, Jun 17, 2015.

E. Coli Testing Market Expected to Reach $2.1 Billion by 2022 
Food Safety News, Jun 23, 2015.

Picking up Protease Allowed Y. Pestis to Cause Pneumonic Plague, Study Finds 
GenomeWeb, Jun 30, 2015.

Finland's Orion Diagnostica Launches C. diff Kit for GenRead Isothermal MDx System in Europe
Johnson M. GenomeWeb, Jun 30, 2015.

What's Old Is New Again: Revolutionary new methods for extracting, purifying, and sequencing ever-more-ancient DNA 
Grant B. The Scientist, Jun 1, 2015.

Field Evaluation of Rapid Ebola Immunoassay Reveals Limitations of PCR-Based Testing
Rizk C. GenomeWeb, Jul 1, 2015.

Antibiotics and the Gut Microbiome
Azvolinsky A. The Scientist, Jun 30, 2015.

Researchers frustrated by failure to roll out 'game-changing' Ebola test Researchers frustrated by failure to roll out 'game-changing' Ebola test
Butler D. Nature, Jun 26, 2015.

Too Many Mitochondrial Genome Papers: And too few insights gleaned from them 
Smith DR. The Scientist, Jun 29, 2015.

A vision for investigating the microbiology of health and disease.
Lipkin WI et al. J. Infect. Dis. 2015 Jul 15. S26-30

Towards genomic prediction of drug resistance in tuberculosis.
Gardy JL et al. Lancet Infect Dis 2015 Jun 23.

Moving toward prime time: Host signatures for diagnosis of respiratory infections.
Tsalik EL et al. J. Infect. Dis. 2015 Jul 15. (2) 173-5

Vaccination and narcolepsy: Immune link found?
Wekerle H. Sci Transl Med, Jul 1, 2015.

Thinking globally, acting locally: harnessing the immune system to deal with recalcitrant pathogens.
Russell MW et al. MBio 2015 (3) e00382-15