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

Genomics|Update|Infectious Diseases

Volume 34  Number 21  May 28 - June 4, 2015

Advanced Molecular Detection in Action

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

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

Antimicrobials, Vaccines, Interventions

Development of live-attenuated arenavirus vaccines based on codon deoptimization.
Cheng B et al. J. Virol. 2015 Apr (7) 3523-33

New approaches for the standardization and validation of a Real-Time qPCR assay using TaqMan probes for quantification of yellow fever virus on clinical samples with high quality parameters.
Fernandes-Monteiro AG et al. Hum Vaccin Immunother 2015 May 26. 0

Risk of drug resistance among persons acquiring HIV within a randomized clinical trial of single- or dual-agent preexposure prophylaxis.
Lehman DA et al. J. Infect. Dis. 2015 Apr 15. (8) 1211-8

The A581G mutation in the gene encoding Plasmodium falciparum dihydropteroate synthetase reduces the effectiveness of sulfadoxine-pyrimethamine preventive therapy in Malawian pregnant women.
Gutman J et al. J. Infect. Dis. 2015 Jun 15. (12) 1997-2005

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Detection and Diagnosis

Histoplasmosis and skin lesions in HIV: a safe and accurate diagnosis.
Moreno-Coutiño G et al. Mycoses 2015 May 25.

Plasma concentration of parasite DNA as a measure of disease severity in falciparum malaria.
Imwong M et al. J. Infect. Dis. 2015 Apr 1. (7) 1128-33

Laboratory diagnosis of noroviruses: present and future.
Pang X et al. Clin. Lab. Med. 2015 Jun (2) 345-362

Molecular methods for identification and characterization of novel papillomaviruses.
Kocjan BJ et al. Clin. Microbiol. Infect. 2015 May 20.

Development of two real-time multiplex PCR assays for the detection and quantification of eight key bacterial pathogens in lower respiratory tract infection.
Gadsby NJ et al. Clin. Microbiol. Infect. 2015 May 13.

Clinical consequences of new diagnostic tools for intestinal parasites.
van Lieshout L et al. Clin. Microbiol. Infect. 2015 Apr 2.

Comparison of a quantitative PCR assay with peripheral blood smear examination for detection and quantitation of Babesia microti infection in humans.
Wang G et al. Diagn. Microbiol. Infect. Dis. 2015 Jun (2) 109-13

Pneumocystis jirovecii in the air surrounding patients with Pneumocystis pulmonary colonization.
Le Gal S et al. Diagn. Microbiol. Infect. Dis. 2015 Jun (2) 137-42

Assay for estimating total bacterial load: relative qPCR normalisation of bacterial load with associated clinical implications.
Brukner I et al. Diagn. Microbiol. Infect. Dis. 2015 May 2.

Validation of a phage-open reading frame typing kit for rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) transmission in a tertiary hospital.
Takahashi H et al. Infect Drug Resist 2015 107-11

Discrepancy in MALDI-TOF MS identification of uncommon Gram-negative bacteria from lower respiratory secretions in patients with cystic fibrosis.
AbdulWahab A et al. Infect Drug Resist 2015 83-8

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Epidemiology, Outbreaks, Transmission

Multinational outbreak of Salmonella enteritidis infection during an international youth ice hockey competition in Riga, Latvia, preliminary report, March and April 2015
Pesola AK, et al. Eurosurveillance, Volume 20, Issue 20, 21 May 2015. 

[HIV-1 subtype diversity and transmission clusters among men having sex with men who recently got HIV-l infection, in Zhejiang province].
Zhang Ji et al. Zhonghua Liu Xing Bing Xue Za Zhi 2015 Jan (1) 61-6

Whole-genome sequencing for outbreak investigations of methicillin-resistant Staphylococcus aureus in the neonatal intensive care unit: time for routine practice?
Azarian T et al. Infect Control Hosp Epidemiol 2015 May 8. 1-9

Evidence of self-sustaining drug resistant HIV-1 lineages among untreated patients in the UK.
Mbisa JL et al. Clin. Infect. Dis. 2015 May 19.

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Evolution, Ecology, Pathogenicity, Populations

Evolutionary trajectories of two distinct avian influenza epidemics: Parallelisms and divergences.
Fusaro A et al. Infect. Genet. Evol. 2015 May 20.

Population structure of Legionella spp. from environmental samples in Gabon, 2013.
Ehrhardt J et al. Infect. Genet. Evol. 2015 May 19.

The complete mitochondrial genome of Pseudoterranova azarasi and comparative analysis with other anisakid nematodes.
Liu Shan-Shan et al. Infect. Genet. Evol. 2015 May 18.

Impact of HBV genotypes A and D genetic variability on infection evolution.
Urone N et al. Infect. Genet. Evol. 2015 May 16.

Genetic diversity and recombination within bufaviruses: Detection of a novel strain in Hungarian bats.
Kemenesi G et al. Infect. Genet. Evol. 2015 May 16.

A novel baseline hepatitis B virus sequencing-based strategy for predicting adefovir antiviral response.
Wang Yu-Wei et al. Infect. Genet. Evol. 2015 May 14. AR

Impact of spatial dispersion, evolution, and selection on Ebola Zaire Virus epidemic waves.
Azarian Taj et al. Sci Rep 2015 10170

Reliable timescale inference of HBV genotype A origin and phylodynamics.
Zehender Gi et al. Infect. Genet. Evol. 2015 Jun 361-9

Genome sequence analysis of Ebola virus in clinical samples from three British healthcare workers, August 2014 to March 2015
Bell A, et al. Eurosurveillance, Volume 20, Issue 20, 21 May 2015.

Genetic diversity of highly pathogenic H5N8 avian influenza viruses at a single overwintering site of migratory birds in Japan, 2014/15
Ozawa M, et al. Eurosurveillance, Volume 20, Issue 20, 21 May 2015.

Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing.
Agoti CN et al. J. Virol. 2015 Apr (7) 3444-54

Filovirus RefSeq entries: evaluation and selection of filovirus type variants, type sequences, and names.
Kuhn JH et al. Viruses 2014 Sep (9) 3663-82 (CDC Author)

Molecular characterization of quinolone resistance mechanisms and extended-spectrum ß-lactamase production in Escherichia coli isolated from dogs.
Meireles D et al. Comp. Immunol. Microbiol. Infect. Dis. 2015 May 12.

Variability of HIV-1 in the female genital reservoir during genital reactivation of herpes simplex virus type 2 (HSV-2).
LeGoff Jérôme et al. Clin. Microbiol. Infect. 2015 May 20.

Prevalence of Stx-producing Shigella species isolated from French Travelers Returning from the Caribbean: An emerging pathogen with international implications.
Gray MD et al. Clin. Microbiol. Infect. 2015 May 13.

Transcriptomic analysis of colistin-susceptible and colistin-resistant isolates identifies genes associated with colistin resistance in Acinetobacter baumannii.
Park Young K et al. Clin. Microbiol. Infect. 2015 Apr 22.

Striking divergence in toxoplasma ROP16 nucleotide sequences from human and meat samples.
Alvarez C et al. J. Infect. Dis. 2015 Jun 15. (12) 2006-13

Changes in the population structure of invasive Neisseria meningitidis in the United States after Quadrivalent Meningococcal Conjugate vaccine licensure.
Wang Xin et al. J. Infect. Dis. 2015 Jun 15. (12) 1887-94 (CDC Author)

Genetic dissection of complete genomes of Type 2 PRRS viruses isolated in Denmark over a period of 15 years.
Kvisgaard LK et al. Vet. Microbiol. 2013 Dec 27. (3-4) 334-44

Nomenclature updates resulting from the evolution of avian influenza A(H5) virus clades 2.1.3.2a, 2.2.1, and 2.3.4 during 2013-2014.
Donis RO et al. Influenza Other Respir Viruses 2015 May 12. (CDC Author)

Rotavirus group A genotypes detected through diarrheal disease surveillance in Haiti, 2012.
Esona MD et al. Am. J. Trop. Med. Hyg. 2015 May 11. (CDC Author)

Variation in Plasmodium falciparum histidine-rich protein 2 (Pfhrp2) and Plasmodium falciparum histidine-rich protein 3 (Pfhrp3) gene deletions in Guyana and Suriname
Okoth SA, et al. PLoS ONE 2015; 10(5): e0126805. (CDC Author)

Haemagglutinin mutations and glycosylation changes shaped the 2012/13 influenza A(H3N2) epidemic, Houston, Texas.
Stucker KM et al. Euro Surveill. 2015 (18) (CDC Author)

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Host-Microbe Interactions

The distribution of parasite strains among hosts affects disease spread in a social insect.
Ulrich Y et al. Infect. Genet. Evol. 2015 Jun 348-53

A host susceptibility gene, DR1, facilitates influenza A virus replication by suppressing host innate immunity and enhancing viral RNA replication.
Hsu Shih-Feng et al. J. Virol. 2015 Apr (7) 3671-82

Influence of host resistance on viral adaptation: hepatitis C virus as a case study.
Plauzolles A et al. Infect Drug Resist 2015 63-74

The cutaneous microbiome in outpatients presenting with acute skin abscesses.
Horton JM et al. J. Infect. Dis. 2015 Jun 15. (12) 1895-904

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Methods

Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION 
Urban JM, et al. bioRxiv, May 13, 2015.

HLAreporter: a tool for HLA typing from next generation sequencing data.
Huang Yi et al. Genome Med 2015 (1) 25

Improved genome inference in the MHC using a population reference graph.
Dilthey A et al. Nat. Genet. 2015 Apr 27.

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Policy

FDA proposes rule to collect antimicrobial sales and distribution data by animal species
FDA, May 19, 2015.

World Health Assembly addresses antimicrobial resistance, immunization gaps and malnutrition
World Health Organization, May 25, 2015.

JAMA Forum: Critical Choices for the WHO After the Ebola Epidemic 
Gostin LO. JAMA, May 27, 2015.

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Reviews, News and Commentaries

Wide use of antibiotics allows C.diff to flourish
Brody J. New York Times, May 26, 2015.

We Need Antibiotics. They're Not Profitable To Make. Who Pays?
(blog post) McKenna M. Phenomena: Germination, nationalgeographic.com, May 23, 2015

FDA clears Roche Cobas C. diff test
GenomeWeb, May 26, 2015.[by free subscription only]

Seegene Gets CE Mark for GI Infectious Disease Test
GenomeWeb, May 26, 2015.[by free subscription only].

Brown University Team Creates Strategy to Increase MinIon Read Lengths
Heger M. GenomeWeb, May 26, 2015.[by paid subscription only]

Antibiotic alternatives rev up bacterial arms race
Reardon S. Nature, May 27, 2015.

Ebola teaches tough lessons about rapid research
Hayden EC. Nature, May 27, 2015.

Molecular Diagnostics: Current Research and Applications
(book review) Adams ER. Clin Infect Dis 2015; 60: 1877.

Improving predictions of the risk of resistance development against new and old antibiotics.
Andersson Dan I et al. Clin. Microbiol. Infect. 2015 May 20

New diagnostic tools in clinical parasitology.
Bottieau E et al. Clin. Microbiol. Infect. 2015 Apr 22.

Massive lineage replacements and cryptic outbreaks of Salmonella Typhi in eastern and southern Africa
Wirth T. Nat Genet, May 27, 2015.