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

Genomics|Update|Infectious Diseases

Volume 35  Number 7  August 12-20, 2015

Advanced Molecular Detection in Action

• News/ Reviews/ Commentaries
• Methods/ Tools
• Evolution/ Ecology/ Populations
• Pathogenicity / Antimicrobial Resistance

• Detection/ Diagnosis
• Epidemiology/ Outbreaks/ Transmission
• Antimicrobials/ Vaccines/ Interventions
• Host-Microbe Interactions

News/ Reviews/ Commentaries

FDA taps DNAnexus to build communal infrastructure for NGS test development
Thomas UG. GenomeWeb, Aug 6, 2015.

Advancing precision medicine by enabling a collaborative informatics community
Kas-Hout T, Litwack D. FDA Voice, Aug 5, 2015.

Get with the program: DIY tips for adding coding to your analysis arsenal 
Perkel JM. The Scientist, Aug 1, 2015.

NIH launches website for new genomic data sharing policy
GenomeWeb, Aug 10, 2015.

CDC earmarks $2.3M for NGS, bioinformatic approaches to combat infectious disease
GenomeWeb, Aug 7, 2015.

The tsetse fly and the test for genomics in Africa
Krol A. Bio-IT World, Aug 6, 2015.

Plethora of respiratory viruses and respiratory virus data.
Storch GA et al. Clin. Infect. Dis. 2015 Aug 4.

How next-generation sequencing and multiscale data analysis will transform infectious disease management.
Pak T et al. Clin. Infect. Dis. 2015 Aug 6.

Interdisciplinarity and infectious diseases: An Ebola case study.
Ezenwa VO et al. PLoS Pathog. 2015 Aug (8) e1004992

Impact of space flight on bacterial virulence and antibiotic susceptibility.
Taylor PW et al. Infect Drug Resist 2015 249-62

The evolution and epidemiology of Listeria monocytogenes in Europe and the United States.
Lomonaco S et al. Infect. Genet. Evol. 2015 Aug 5.

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Methods/Tools

Informatics for RNA sequencing: A web resource for analysis on the cloud.
Griffith M et al. PLoS Comput. Biol. 2015 Aug (8) e1004393

How current direct-acting antiviral and novel cell culture systems for HCV are shaping therapy and molecular diagnosis of chronic HCV infection.
Maggi F et al. Curr Drug Targets 2015 Aug 6.

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Evolution/ Ecology/ Populations

The two-phase emergence of non pandemic HIV-1 group O in Cameroon.
Leoz M et al. PLoS Pathog. 2015 Aug (8) e1005029

Newly emerged porcine deltacoronavirus associated with diarrhoea in swine in China: Identification, prevalence and full-length genome sequence analysis.
Song D et al. Transbound Emerg Dis 2015 Aug 6.

Origin and evolution of Nipah virus.
Presti AL et al. J. Med. Virol. 2015 Aug 7.

Genotype-specific variation in West Nile virus dispersal in California.
Duggal NK et al. Virology 2015 Jul 23. 79-85 (CDC Author)

The human gut microbiome as a transporter of antibiotic resistance genes between continents.
Bengtsson-Palme J et al. Antimicrob. Agents Chemother. 2015 Aug 10. 

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Pathogenicity / Antimicrobial Resistance

A molecular trigger for intercontinental epidemics of group A Streptococcus.
Zhu L et al. J. Clin. Invest. 2015 Aug 10. 

Adaptive evolution of malaria parasites in French Guiana: Reversal of chloroquine resistance by acquisition of a mutation in pfcrt
Pelleau S, et al. PNAS, Aug 10, 2015.

Gag-protease sequence evolution following protease inhibitor monotherapy treatment failure in HIV-1 viruses circulating in East Africa.
Sutherland KA et al. AIDS Res. Hum. Retroviruses 2015 Aug 10.

Single genome analysis for the detection of linked multiclass drug resistance mutations in HIV-1-infected children after failure of protease inhibitor-based first-line therapy.
Lange CM et al. J. Acquir. Immune Defic. Syndr. 2015 Jun 1. (2) 138-44

Complete genome sequence of enteroinvasive Escherichia coli O96:H19 associated with a severe foodborne outbreak.
Pettengill EA et al. Genome Announc 2015 (4)

Immunoproteomic profiling of Rickettsia parkeri and Rickettsia amblyommii.
Pornwiroon W et al. Ticks Tick Borne Dis 2015 Jul 22. (CDC Author)

Virology, immunology and pathology of human rabies during treatment.
Caicedo Y et al. Pediatr. Infect. Dis. J. 2015 May (5) 520-8 (CDC Author)

Identification of mutations conferring streptomycin resistance in multidrug-resistant tuberculosis of China.
Zhao Li-Li et al. Diagn. Microbiol. Infect. Dis. 2015 Jul 2.

Fitness inference from short-read data: within-host evolution of a reassortant H5N1 influenza virus.
Illingworth CJR et al. Mol. Biol. Evol. 2015 Aug 4.

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Detection/ Diagnosis

Development and validation of digital ELISAs for ultrasensitive detection and quantification of C. difficile toxins in stool.
Song L et al. J. Clin. Microbiol. 2015 Jul 22.

Molecular detection and characterization of Mycoplasma pneumoniae among patients hospitalized with community-acquired pneumonia in the United States
Diaz MH, et al. Open Forum Infect Dis, Jul 16, 2015. (CDC Author)

Development and evaluation of an enterovirus D68 real-time reverse transcriptase PCR assay.
Wylie TN et al. J. Clin. Microbiol. 2015 Aug (8) 2641-7

Human toxoplasmosis: a comparative evaluation of the diagnostic potential of recombinant Toxoplasma gondii ROP5 and ROP18 antigens.
Grzybowski MM et al. J. Med. Microbiol. 2015 Aug 3.

DNA-microarray-based genotyping of Clostridium difficile.
Gawlik D et al. BMC Microbiol. 2015 158

A lab-on-chip based platform for fast molecular diagnosis of multi-drug resistant tuberculosis.
Cabibbe AM et al. J. Clin. Microbiol. 2015 Aug 5.

High Resolution Melting-Typing (HRMT) of methicillin-resistant Staphylococcus aureus (MRSA): The new frontier to replace multi-locus sequence typing (MLST) for epidemiological surveillance studies.
Mongelli G0 et al. J. Microbiol. Methods 2015 Aug 5.

Analysis of methicillin-resistant Staphylococcus aureus major clonal lineages by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS).
Zhang T et al. J. Microbiol. Methods 2015 Aug 5. 122-127

Novel poxvirus infection in an immune suppressed patient.
Lakis NS et al. Clin. Infect. Dis. 2015 Aug 3. (CDC Author)

Bartonella spp. and Coxiella burnetii associated with community-acquired, culture-negative endocarditis, Brazil.
Siciliano RF et al. Emerging Infect. Dis. 2015 Aug (8) 1429-32 (CDC Author)

Enhanced detection of type C botulinum neurotoxin by the Endopep-MS assay through optimization of peptide substrates.
Wang D et al. Bioorg. Med. Chem. 2015 Jul 1. (13) 3667-73 (CDC Author)

Application of bioinformatics in probe design enables detection of enteroviruses on different taxonomic levels by advanced in situ hybridization technology.
Laiho JE et al. J. Clin. Virol. 2015 Aug 165-71 (CDC Author)

Pyrosequencing for rapid detection of Mycobacterium tuberculosis second-line drugs and ethambutol resistance.
Lacoma A et al. Diagn. Microbiol. Infect. Dis. 2015 Jul 11.

Detection of enteropathogens associated with travelers' diarrhea using a multiplex Luminex-based assay performed on stool samples smeared on Whatman FTA Elute cards.
Lalani T et al. Diagn. Microbiol. Infect. Dis. 2015 Sep (1) 18-20

Molecular detection of novel Anaplasmataceae closely related to Anaplasma platys and Ehrlichia canis in the dromedary camel (Camelus dromedarius).
Bastos ADS et al. Vet. Microbiol. 2015 Sep 30. (3-4) 310-4

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Epidemiology/ Outbreaks/ Transmission

Community surveillance of respiratory viruses among families in the Utah Better Identification of Germs-Longitudinal Viral Epidemiology (BIG-LoVE) study.
Byington CL et al. Clin. Infect. Dis. 2015 Aug 4.

Importance of molecular typing in confirmation of the source of a national hepatitis A virus outbreak in Norway and the detection of a related cluster in Germany.
Guzman-Herrador BR et al. Arch. Virol. 2015 Aug 7.

Genetic characterization of multiple hepatitis C virus infections following acute infection in HIV-infected MSM.
Thomas XV et al. AIDS 2015 Aug 7.

Methamphetamine injecting is associated with phylogenetic clustering of hepatitis C virus infection among street-involved youth in Vancouver, Canada.
Cunningham EB et al. Drug Alcohol Depend 2015 Jul 1. 272-6

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Antimicrobials/ Vaccines/ Interventions

Detection and characterization of clade 1 reassortant H5N1 viruses isolated from human cases in Vietnam during 2013.
Thor SW et al. PLoS ONE 2015 (8) e0133867

A cluster randomised trial introducing rapid diagnostic tests into registered drug shops in Uganda: Impact on appropriate treatment of malaria.
Mbonye AK et al. PLoS ONE 2015 (7) e0129545

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Host-Microbe Interactions

Host genetic variants influencing the clinical course of hepatitis C virus infection.
Matsuura K et al. J. Med. Virol. 2015 Jul 25.

Spontaneous clearance of the hepatitis C virus among men who have sex with men.
Seaberg EC et al. Clin. Infect. Dis. 2015 Jul 14.

Possible role of TLR4 and TLR9 SNPs in protection against congenital toxoplasmosis.
Wujcicka W et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Aug 9.

Variants in the mannose-binding lectin gene MBL2 do not associate with sepsis susceptibility or survival in a large European cohort.
Mills TC et al. Clin. Infect. Dis. 2015 May 12.

Multi-center comparison of lung and oral microbiomes of HIV-infected and HIV-uninfected individuals.
Beck JM et al. Am. J. Respir. Crit. Care Med. 2015 Aug 6.