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

Genomics|Update|Infectious Diseases

Volume 35  Number 6  August 5-13, 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

At AACC, clinical labs air concerns regarding FDA's draft LDT guidance

GenomeWeb, Jul 31, 2015.

Risk of "leaky" vaccines debated

Kupferschmidt K. Science, Jul 31, 2015.

Genetic surveillance study finds flu viruses at two US swine markets

GenomeWeb, Jul 31, 2015.

Research scientists to use network much faster than internet

Markoff J. New York Times, Jul 31, 2015.

Researchers turn to NGS to understand growing threat of antibiotic resistance in pathogens

Heger M. GenomeWeb, Jul 29, 2015

UC Berkeley scientists develop ultrafast thermocycling with point-of-care PCR potential

Han A. GenomeWeb, Aug 3, 2015.

California precision medicine effort awards $2.4M to pediatric cancer, infectious disease projects

GenomeWeb, Aug 4, 2015.

UCSF's one-size-fits-all precision medicine test for infection

Keshavan M. MedCityNews, Aug 4, 2015.

Johns Hopkins researchers develop handheld chlamydia test using microfluidics, smartphone

Johnson M. GenomeWeb, Jul 29, 2015.

NASA team readies MinION for sequencing tests aboard ISS; launch scheduled for March 2016

Karow J. GenomeWeb, Jul 29, 2015.

Extreme weight loss surgery works, but is it thanks to the knife--or the microbes?

Leslie M. Science, Aug 4, 2015.

This little piggy went to market-but perhaps should have stayed home.

Webby R et al. Clin. Infect. Dis. 2015 Jul 29.

Plague or anthrax on the subway? Think again, says now-corrected study

Keith R. Retraction Watch (blog), Jul 31, 2015.

Host-directed therapies for tackling multi-drug resistant TB - learning from the Pasteur-Bechamp debates.

Zumla A et al. Clin. Infect. Dis. 2015 Jul 28.

A novel advanced laboratory diagnosis to guide tuberculosis drug therapy.

Amaral L et al. Recent Pat Antiinfect Drug Discov 2015 Aug 3.

Molecular studies on ancient M. tuberculosis and M. leprae: methods of pathogen and host DNA analysis.

Witas HW et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Jul 26.

Future directions for the European influenza reference laboratory network in influenza surveillance

Goddard N, et al. Euro Surveill, Jul 30, 2015.

Real-time digital pathogen surveillance -- the time is now

Gardy J, et al. Genome Biol, Jul 30, 2015.

How Ebola-vaccine success could reshape clinical-trial policy

Butler D, et al. Nature, Aug 4, 2015.

Ebola: Embed research in outbreak response

Lang T. Nature, Aug 5, 2015.

Time for T? Immunoinformatics addresses vaccine design for neglected tropical and emerging infectious diseases.

Terry FE et al. Expert Rev Vaccines 2015 Jan (1) 21-35

Bioinformatics of antimicrobial resistance in the age of molecular epidemiology.

McArthur AG et al. Curr. Opin. Microbiol. 2015 Jul 31. 45-50

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Methods/Tools

Circlator: automated circularization of genome assemblies using long sequencing reads

Hunt M, et al. bioRxiv, Jul 30, 2015.

Application of the multifactor dimensionality reduction method in evaluation of the roles of multiple genes/enzymes in multidrug-resistant acquisition in Pseudomonas aeruginosa strains.

Yao Z et al. Epidemiol. Infect. 2015 Aug 3. 1-

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Evolution/ Ecology/ Populations

Live animal markets in Minnesota: a potential source for emergence of novel influenza A viruses and interspecies transmission.

Choi MJ et al. Clin. Infect. Dis. 2015 Jul 29. (CDC Author)

Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics 

Califf K, et al. Microbial Genomics, Jul 1, 2015.

Phylogenetic characterization of Central-Southern European lineage 2 West Nile virus: Analysis of human outbreaks in Italy and Greece, 2013-2014.

Barzon L et al. Clin. Microbiol. Infect. 2015 Jul 30.

Temporal trends and clonal diversity of penicillin non-susceptible pneumococci from meningitis cases from 1996 to 2012, in Salvador, Brazil.

Dos Santos MS et al. BMC Infect. Dis. 2015 302

Highly virulent non-O157 EHEC serotypes reflect a similar phylogenetic lineage, giving new insights into the evolution of EHEC.

Eichhorn I et al. Appl. Environ. Microbiol. 2015 Jul 31.

Virus isolation, genetic characterization, and seroprevalence of Toscana virus in Algeria.

Alkan C et al. Clin. Microbiol. Infect. 2015 Jul 30. 

Detection of the NS3 Q80K polymorphism by Sanger and deep sequencing in hepatitis C virus (HCV) genotype 1a strains in the United Kingdom.

Beloukas A et al. Clin. Microbiol. Infect. 2015 Jul 29.

Genomic resolution of an aggressive, widespread, diverse and expanding meningococcal serogroup B, C and W lineage.

Lucidarme J et al. J. Infect. 2015 Jul 28.

Genomic sequence of the aflatoxigenic filamentous fungus Aspergillus nomius.

Moore GG et al. BMC Genomics 2015 (1) 551

Genomic analyses of pneumococci reveal a wide diversity of bacteriocins - including pneumocyclicin, a novel circular bacteriocin.

Bogaardt C et al. BMC Genomics 2015 (1) 554

Influenza A viruses of human origin in swine, Brazil.

Nelson MI et al. Emerging Infect. Dis. 2015 Aug (8) 1339-47

Genome of emerging norovirus GII.17, United States, 2014.

Parra GI et al. Emerging Infect. Dis. 2015 Aug (8) 1477-9

Schmallenberg virus recurrence, Germany, 2014.

Wernike K et al. Emerging Infect. Dis. 2015 Jul (7) 1202-4

A globally distributed mobile genetic element inhibits natural transformation of Vibrio cholerae.

Dalia AB et al. Proc. Natl. Acad. Sci. U.S.A. 2015 Aug 3.

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri.

Connor TR et al. Elife 2015 

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Pathogenicity / Antimicrobial Resistance

Applying phylogenomics to understand the emergence of Shiga Toxin producing Escherichia coli O157:H7 strains causing severe human disease in the United Kingdom

Dallman T, et al. Microbial Genomics, Jul 27, 2015. 

Region specific diversification of the highly virulent serotype 1 streptococcus pneumoniae 

Cornick JE, et al. Microbial Genomics, Jul 20, 2015.

Enteropathogenic and enteroaggregative E. coli in stools of children with acute gastroenteritis in Davidson County, Tennessee

Foster MA, et al. Diagn Microbiol Infect Dis, Jul 26, 2015. (CDC Author)

Cloacibacillus sp., a potential human pathogen associated with bacteremia in Quebec and New Brunswick.

Domingo M-C et al. J. Clin. Microbiol. 2015 Jul 29.

Disease burden of invasive meningococcal disease in the Netherlands between June 1999 and June 2011: A subjective role for serogroup and clonal complex.

Stoof SP et al. Clin. Infect. Dis. 2015 Jun 29.

Clinical manifestations and genetic variation of Leishmania infantum and Leishmania tropica in Southern Turkey.

Eroglu F et al. Exp. Parasitol. 2015 Jul 67-74

Comparison of asymptomatic and symptomatic rhinovirus infections in university students: incidence, species diversity, and viral load.

Granados A et al. Diagn. Microbiol. Infect. Dis. 2015 Aug (4) 292-6

Genetic characterization of highly pathogenic avian influenza A(H5N6) virus, Guangdong, China [letter]

Mok CPK, et al. Emerg Infect Dis, Dec 2015. 

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Detection/ Diagnosis

Is PCR the next reference standard for the diagnosis of schistosoma in stool? A comparison with microscopy in Senegal and Kenya.

Meurs L et al. PLoS Negl Trop Dis 2015 Jul (7) e0003959

Molecular method for the detection of Andes hantavirus infection: validation for clinical diagnostics

Vial C, et al. Diagn Microbiol Infect Dis, Jul 29, 2015.

Rapid detection of B2-ST131 clonal group of extended-spectrum beta-lactamase-producing escherichia coli by matrix-assisted laser desorption ionization-time of flight mass spectrometry: Discovery of a peculiar amino acid substitution in B2-ST131 clonal group

Nakamura A, et al. Diagn Microbiol Infect Dis, Jul 29, 2015.

Polymerase chain reaction, pyrosequencing, and culture of infected and uninfected site skin biopsy specimens cannot identify etiology of cellulitis 

Crisp JG, et al. Clin Infect Dis, Aug 3, 2015.

International mycoplasma pneumoniae typing study: interpretation of M. pneumoniae multilocus variable-number tandem-repeat analysis.

Chalker VJ et al. New Microbes New Infect 2015 Sep 37-40

The evaluation of seven commercial real-time PCR kits for Zaire Ebolavirus using virus-like particles encapsulated EBOV RNA

Wang G, et al. Diagn Microbiol Infect Dis, Aug 1, 2015.

Genomic assays for identification of chikungunya virus in blood donors, Puerto Rico, 2014.

Chiu CY et al. Emerging Infect. Dis. 2015 Aug (8) 1409-13

Direct identification of major gram-negative pathogens in respiratory specimens by respiFISH® HAP Gram (-) Panel, a beacon-based FISH methodology.

Koncan R et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Jul 29.

Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires' disease incidents.

Moran-Gilad J et al. Euro Surveill. 2015 (28)

Differentiation of acinetobacter genomic species 13BJ/14TU from acinetobacter haemolyticus using MALDI - TOF MS.

Toh BE et al. J. Clin. Microbiol. 2015 Jul 29.

The Rapid-Heat LAMPellet Method: A potential diagnostic method for human urogenital schistosomiasis.

Gandasegui J et al. PLoS Negl Trop Dis 2015 Jul (7) e0003963

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Epidemiology/ Outbreaks/ Transmission

A year of infection in the intensive care unit: prospective whole genome sequencing of bacterial clinical isolates reveals cryptic transmissions and novel microbiota.

Roach DJ et al. PLoS Genet. 2015 Jul (7) e1005413

Outbreak of salmonella enteritidis phage type 13a infection in Sweden linked to imported dried-vegetable spice mixes, December 2014 to July 2015

Jernberg C, et al. Euro Surveill 2015;20(30):pii=21194.

Long-lasting outbreak of erythromycin- and ciprofloxacin-resistant campylobacter jejuni subspecies jejuni From 2003 to 2013 in men who have sex with men, Quebec, Canada.

Gaudreau C et al. Clin. Infect. Dis. 2015 Jul 17.

Profile of the HIV epidemic in Cape Verde: molecular epidemiology and drug resistance mutations among HIV-1 and HIV-2 infected patients from distinct islands of the archipelago.

de Pina-AI et al. PLoS ONE 2014 (4) e96201

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Antimicrobials/ Vaccines/ Interventions

Diversion of HIV-1 vaccine-induced immunity by gp41-microbiota cross-reactive antibodies

Williams WB, et al. Science, Jul 30, 2015.

HIV-1 subtype diversity among clinical specimens submitted for routine antiviral drug resistance testing in the United States

Germer JJ, et al. Diagn Microbiol Infect Dis, Jul 26, 2015.

Protection against dengue disease by synthetic nucleic acid antibody prophylaxis/immunotherapy.

Flingai S et al. Sci Rep 2015 12616

Pretreatment HIV drug resistance increases regimen switches in sub-saharan Africa

Boender TS, et al. Clin Infect Dis, Aug 3, 2015.

HIV-1 VACCINES. Priming a broadly neutralizing antibody response to HIV-1 using a germline-targeting immunogen.

Jardine JG et al. Science 2015 Jul 10. (6244) 156-61

Using epidemics to map H3 equine influenza virus determinants of antigenicity.

Woodward A et al. Virology 2015 Jul 187-98

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Host-Microbe Interactions

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

Korem T, et al. Science, Jul 30, 2015.

The effect of antibiotics on the microbiome in acute exacerbations of chronic rhinosinusitis.

Merkley MA et al. Int Forum Allergy Rhinol 2015 Jul 30.

Fitness-balanced escape determines resolution of dynamic founder virus escape processes in HIV-1 infection.

Sunshine JE et al. J. Virol. 2015 Jul 29.

Bioinformatic analysis of neurotropic HIV envelope sequences identifies polymorphisms in the gp120 bridging sheet that increase macrophage-tropism through enhanced interactions with CCR5.

Mefford ME et al. Virology 2015 Jul 210-22