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

Genomics|Update|Infectious Diseases

Volume 34  Number 4  January 29 - February 5, 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

Ultradeep pyrosequencing of NS3 to predict response to triple therapy with protease inhibitors in previously treated chronic hepatitis C patients
Larrat S, et al.  J Clin Microbiol 2015; 53(2):389-397.

Viral genetic diversity and polymorphisms in a cohort of HIV-1 infected patients eligible for the initiation of antiretroviral therapy in Abuja, Nigeria.
Yang C, et al. AIDS Res Hum Retroviruses. 2015 Jan 12.

Safety and immunogenicity of DNA vaccines encoding Ebolavirus and Marburgvirus wild-type glycoproteins in a phase I clinical trial
Sarwar UN, et al. J Infect Dis 2015; 211 (4): 549-557.

Live virus vaccines based on a yellow fever vaccine backbone: standardized template with key considerations for a risk/benefit assessment
Monath TP, et al. Vaccine. 2015 Jan 1;33(1):62-72.

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Detection and Diagnosis

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

Novel multiplex format of an extended multilocus variable-number-tandem-repeat analysis of Clostridium difficile correlates with tandem repeat sequence typing 
Jensen MB, et al. J Microbiol Methods. 2015 Jan 22.

DNA microarray-based PCR ribotyping of Clostridium difficile
Schneeberg A, et al. J Clin Microbiol 2015; 53(2):433-442.

Development of a rapid multiplex PCR assay to genotype Pasteurella multocida strains by use of the lipopolysaccharide outer core biosynthesis locus
Harper M, et al. J Clin Microbiol 2015; 53(2):477-485.

Development of a multiple-locus variable-number tandem-repeat typing scheme for genetic fingerprinting of Burkholderia cenocepacia and application to nationwide epidemiological analysis
Segonds C, et al. J Clin Microbiol 2015; 53(2):398-409.

Gordonia species as emerging causes of continuous-ambulatory-peritoneal-dialysis-related peritonitis identified by 16S rRNA and secA1 gene sequencing and matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS)
Lam JY, et al. J Clin Microbiol 2015; 53(2):671-676.

High-throughput mycobacterial interspersed repetitive-unit–variable-number tandem-repeat genotyping for Mycobacterium tuberculosis epidemiological studies
Gauthier M, et al. J Clin Microbiol 2015; 53(2):498-503.

A diagnostic HIV-1 tropism system based on sequence relatedness
Edwards S, et al. J Clin Microbiol 2015; 53(2):597-610.

Accurate quantification of episomal HIV-1 two-long terminal repeat circles by use of optimized DNA isolation and droplet digital PCR
Malatnikova E, et al. J Clin Microbiol 2015; 53(2):699-701.

Use of matrix-assisted laser desorption ionization–time of flight mass spectrometry for identification of molds of the Fusarium genus
Triest D, et al. J Clin Microbiol 2015; 53(2):465-476.

Design and evaluation of peptide nucleic acid probes for specific identification of Candida albicans
Kim HJ, Brehm-Stecher BF. J Clin Microbiol 2015; 53(2): 511-521.

Microsatellite (STRAf) genotyping cannot differentiate between invasive and colonizing Aspergillus fumigatus isolates
Escribano P, et al. J Clin Microbiol 2015; 53(2):667-670.

Isolation and enrichment of Cryptosporidium DNA and verification of DNA purity for whole-genome sequencing
Guo Y, et al. J Clin Microbiol 2015; 53(2):641-647.

Comparison of matrix-assisted laser desorption ionization–time of flight mass spectrometry and molecular biology techniques for identification of Culicoides (Diptera: Ceratopogonidae) biting midges in Senegal
Sambou M, et al. J Clin Microbiol 2015; 53(2):410-418.

Diagnosis of community-acquired acute respiratory illness: From conventional microbiological methods to molecular detection (multiplex)
Bouvet D, et al. Pathol Biol (Paris). 2015 Jan 13.

Reducing time to identification of positive blood cultures with MALDI-TOF MS analysis after a 5-h subculture
Verroken A, et al. Eur J Clin Microbiol Infect Dis. 2015 Feb;34(2):405-13.

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.

First experience of a multicenter external quality assessment of molecular 16S rRNA gene detection in bone and joint infections
Plouzeau C, et al. J Clin Microbiol 2015; 53(2):419-424.

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Epidemiology, Outbreaks, Transmission

Genomic dissection of travel-associated extended-spectrum-beta-lactamase-producing Salmonella enterica Serovar Typhi Isolates Originating from the Philippines: a one-off occurrence or a threat to effective treatment of typhoid fever?
Hendriksen RS, et al. J Clin Microbiol 2015; 53(2): 677-680.

An atypical outbreak of food-borne botulism due to Clostridium botulinum Types B and E from ham
Mazuet C, et al. J Clin Microbiol 2015; 53(2): 722-726.

Molecular and epidemiological review of toxigenic Diphtheria infections in England between 2007 and 2013
Both L, et al. J Clin Microbiol 2015; 53(2): 567-572.

Investigating the epidemiology of repeat Chlamydia trachomatis detection after treatment by using C. trachomatis OmpA genotyping
Kapil R, et al. J Clin Microbiol 2015; 53(2): 546-549.

Evolution of cocirculating varicella-zoster virus genotypes during a chickenpox outbreak in Guinea-Bissau
Depledge DP, et al. J Virol. 2014 Dec;88(24):13936-46.

Asymptomatic malaria infections: detectability, transmissibility and public health relevance
Bousema T, et al. Nat Rev Microbiol. 2014 Dec;12(12):833-40.

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Evolution, Ecology, Pathogenicity, Populations

Genetic characterization of Shigella flexneri Isolates in Guizhou Province, China
Li S, et al. PLoS One 2015 Jan 24;10(1):e0116708.

Draft genome sequence of Legionella pneumophila D-5864, a serogroup 6 strain
Morrison SS, et al. Genome Announc 2015 ;3(1).

Dissemination of high-risk clones of extensively drug-resistant Pseudomonas aeruginosa in Colombia
Correa A, et al. Antimicrob Agents Chemother. 2015 Jan 20.

Epidemic clones, oceanic gene pools and eco-LD in the free living marine pathogen Vibrio parahaemolyticus
Cui Y, et al. Mol Biol Evol. 2015 Jan 19.

Local evolutionary patterns of human respiratory syncytial virus derived from whole genome sequencing
Agoti CN, et al. J Virol. 2015 Jan 21.

Recent population expansions of hepatitis B virus in the United States
Ramachandran S, et al. J Virol. 2014 Dec;88(24):13971-80.

Complete genome sequence of MneRV2, the pig-tailed macaque RV2 rhadinovirus, and evolutionary relationship with rhesus macaque RRV and human herpesvirus 8/KSHV
Bruce AG, et al. J Virol. 2015 Jan 21.

Proteomics analyses for the global proteins in the brain tissues of different human prion diseases
Shi Q, et al. Mol Cell Proteomics. 2015 Jan 23.

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Host-Pathogen Interactions

A new method for estimating species age supports the co-existence of malaria parasites and their mammalian hosts 
Silva JC, et al. Mol Biol Evol. 2015 Jan 13.

Comment: 
U of Maryland-led statistical study points to co-evolution of Plasmodium parasite, mammalian hosts 
Thomas UG. GenomeWeb, Jan 26, 2015.

Genomic assays for Epstein–Barr virus-positive gastric adenocarcinoma
Gulley ML Exp Mol Med. 2015 Jan 23;47:e134.

Microbiota that affect risk for Shigellosis in children in low-income countries
Lindsay B, et al. Emerg Infect Dis. 2015 Feb;21(2):242-250.

Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism
Hu Z, et al. Nat Genet 2015; 47: 158–163.

RNA populations in immunocompromised patients as reservoirs for novel norovirus variants
Vega E, et al. J Virol. 2014 Dec;88(24):14184-96.

Commensal microbes and interferon-λ determine persistence of enteric murine norovirus infection
Baldridge MT, et al. Science. 2015 Jan 16;347(6219):266-9.

HIV-1 adaptation to HLA: a window into virus–host immune interactions 
Carlson JM, et al. Trends Microbiol, Jan 19, 2015.

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Methods

Bayesian models for syndrome- and gene-specific probabilities of novel variant pathogenicity
Ruklisa D, et al. Genome Med 2015; 7:5.

Comment:
Variant interpretation through Bayesian fusion of frequency and genomic knowledge
Shaw CA, Campbell IM. Genome Med 2015; 7:4.  

Methods of integrating data to uncover genotype–phenotype interactions
Ritchie MD, et al. Nat Rev Genet 2015; 16: 85–97.

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Policy

Potential risks and benefits of gain-of-function research:  Summary of a workshop (book) 
National Research Council and National Institute of Medicine.  2015.

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Reviews, News and Commentaries

Mystery childhood paralysis stumps researchers
Ewen Callaway, Nature News, Jan 28, 2015

Use of MDx tests for animal health on the rise, but cost concerns present significant hurdle
Johnson M. GenomeWeb, Jan 26, 2015.

Colorado researchers study 'superbug' for antibiotic resistance on farms
Reuters, Jan 16, 2015.

Ebola vaccine to be tested on 30 000 volunteers
Gulland A. BMJ 2015;350:h448.

Tekmira aims to follow path blazed in HCV to tackle HBV
GenomeWeb, Jan 26, 2015.

Taiwanese firm developing optoelectronic single-molecule sequencing platform
Karow J. GenomeWeb, Jan 27, 2015.

The new scientific revolution: Reproducibility at last
Achenbach J. Washington Post, Jan 27, 2015.

Scientists want to release millions of genetically-modified mosquitos in Florida. Here's why.
Thielking M. Vox, Jan 26, 2015.

Nanopore sequencing for clinical diagnostics
Jones B. Nat Rev Genet 2015; 16: 68.

Recombination: genomic mix 'n' match
Boinett CJ, Cain AK. Nat Rev Microbiol. 2014 Dec;12(12):795.

Melioidosis diagnostic workshop, 2013
Hoffmaster AR, et al. Emerg Infect Dis 2015 Feb;21(2).

Climate change and infectious disease: time for a new normal?
Heffernan C. Lancet Infect Dis 2015; 15(2): 143–144.

How the current West African Ebola virus disease epidemic is altering views on the need for vaccines and is galvanizing a global effort to field-test leading candidate vaccines
Levine MM, et al. J Infect Dis 2015; 211(4): 504-507.