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

Genomics|Update|Infectious Diseases

Volume 35  Number 5  July 30 - August 6, 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

Wayne State awarded $4.8M grant to optimize antibiotic use for drug-resistant infections 
GenomeWeb, Jul 27, 2015.

Imperfect poultry vax
Keener AB. The Scientist, Jul 27, 2015.

Drug-resistant bacteria possess natural ability to become vulnerable to antibiotics
(news release) Washington Univ St. Louis, Jul 13, 2015.

SNP test aims to ID patients who may spontaneously clear HCV
Johnson M. GenomeWeb, Jul 22, 2015.

AACC 2015: New mobile DNA test for chlamydia announced
Bushey R. Bioscience Tech, Jul 29, 2015.

The Genesis Engine (Crispr)
Maxmen A. Wired, Jul 2015.

Point-of-care testing for respiratory viruses in adults: the current landscape and future potential.
Brendish NJ et al. J. Infect. 2015 Jul 24.

Ebola virus disease: experience and decision making for the first patients outside of Africa.
Stephens DS et al. PLoS Med. 2015 Jul (7) e1001857

The individualised versus the public health approach to treating Ebola.
Boyles TH et al. PLoS Med. 2015 Jul (7) e1001858

Genomic epidemiology: Revealing hidden reservoirs for Klebsiella pneumoniae.
Manges AR et al. Clin. Infect. Dis. 2015 Jul 22.

Near full control of human papillomavirus vaccine types.
Dillner J et al. Lancet Infect Dis 2015 Jul 17.

Bringing fungal infections in from the cold
Sekkides O. Lancet Infect Dis 2015;15:884-885.

Expanding the molecular toolkit for chlamydia.
Hybiske K et al. Cell Host Microbe 2015 Jul 8. (1) 11-3

Top of Page

---

Policy

Preliminary guidance related to informed consent for research on dried blood spots obtained through newborn screening 
National Institutes of Health. Notice Number: NOT-OD-15-127, Jul 23, 2015.

Secret service: Government labs should be subject to the same transparent oversight as academic facilities 
(editorial) Nature, Jul 29, 2015.

Top of Page

---

Methods/Tools

Three minimal sequences found in Ebola virus genomes and absent from human DNA.
Silva RM et al. Bioinformatics 2015 Aug 1. (15) 2421-5

MeDuSa: a multi-draft based scaffolder.
Bosi E et al. Bioinformatics 2015 Aug 1. (15) 2443-51

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.
Kelly BJ et al. Bioinformatics 2015 Aug 1. (15) 2461-8

Neutral models of microbiome evolution.
Zeng Q et al. PLoS Comput. Biol. 2015 Jul (7) e1004365

Phylogenetic assignment of Mycobacterium tuberculosis Beijing clinical isolates in Japan by maximum a posteriori estimation.
Seto J et al. Infect. Genet. Evol. 2015 Jul 25.

Top of Page

---

Evolution/ Ecology/ Populations

Genomic characterization of a persistent rubella virus from a case of Fuch' uveitis syndrome in a 73 year old man.
Abernathy E et al. J. Clin. Virol. 2015 Aug 104-9

Natural rabies infection in a domestic fowl (Gallus domesticus): A report from India.
Baby J et al. PLoS Negl Trop Dis 2015 Jul (7) e0003942

Independent emergence of the cosmopolitan Asian chikungunya virus, Philippines 2012.
Tan Kim-K et al. Sci Rep 2015 12279

The Chagas disease domestic transmission cycle in Guatemala: parasite-vector switches and lack of mitochondrial co-diversification between Triatoma dimidiata and Trypanosoma cruzi subpopulations suggest non-vectorial parasite dispersal across the Motagua valley.
Pennington PM et al. Acta Trop. 2015 Jul 24.

Molecular epidemiology and evolution of influenza viruses circulating within European swine between 2009 and 2013.
Watson SJ et al. J. Virol. 2015 Jul 22.

Characterisation of hepatitis C virus recombination in Cameroon using non-specific next generation sequencing.
Iles James C et al. J. Clin. Microbiol. 2015 Jul 22.

Genomic, phylogenetic, and recombinational characterization of herpes simplex virus 2 strains.
Kolb AW et al. J. Virol. 2015 Jun (12) 6427-34

Top of Page

---

Pathogenicity / Antimicrobial Resistance

Longitudinal genetic characterization reveals that cell proliferation maintains a persistent HIV type 1 DNA pool during effective HIV therapy.
von Stockenstrom S et al. J. Infect. Dis. 2015 Aug 15. (4) 596-607

Intermingled Klebsiella pneumoniae populations between retail meats and human urinary tract infections.
Davis GS et al. Clin. Infect. Dis. 2015 Jul 22.

Outcomes and susceptibility to neuraminidase inhibitors in individuals infected with different influenza B lineages: the influenza resistance information study.
van der Vries E et al. J. Infect. Dis. 2015 Jul 9. 

Characterization of antibiotic resistance gene abundance and microbiota composition in feces of organic and conventional pigs from four EU countries.
Gerzova L et al. PLoS ONE 2015 (7) e0132892

Characterization of Escherichia coli-producing extended-spectrum β-Lactamase (ESBL) Isolated from Chicken Slaughterhouses in South Korea.
Lim Jong-Soo et al. Foodborne Pathog. Dis. 2015 Jul 28.

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.
Holt KE et al. Proc. Natl. Acad. Sci. U.S.A. 2015 Jul 7. (27) E3574-81

Deep sequencing and phylogenetic analysis of variants resistant to interferon-based protease inhibitor therapy in chronic hepatitis induced by genotype 1b hepatitis C virus.
Sato M et al. J. Virol. 2015 Jun (11) 6105-16

Top of Page

---

Detection/ Diagnosis

Accurate Detection of Binary Toxin Producer from Clostridium difficile by Matrix-assisted Laser Desorption/ionization Time-of-flight Mass Spectrometry
Kuo SF, et al. Diagn Microbiol Infect Dis, Jul 23, 2015.

Comparison of multilocus sequence typing, RAPD, and MALDI-TOF mass spectrometry for typing of ?-lactam-resistant Klebsiella pneumoniae strains.
Sachse Svea et al. Diagn. Microbiol. Infect. Dis. 2014 Dec (4) 267-71

Clinical Specimen-Direct LAMP: A Useful Tool for the Surveillance of blaOXA-23-Positive Carbapenem-Resistant Acinetobacter baumannii.
Yamamoto Norihisa et al. PLoS ONE 2015 (7) e0133204

"Paper Machine" for Molecular Diagnostics.
Connelly John T et al. Anal. Chem. 2015 Jul 13.

Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip.
Shaffer SM et al. Lab Chip 2015 Jul 14. (15) 3170-82

A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium.
Wuyts V et al. Appl. Microbiol. Biotechnol. 2015 Jul 25.

Whole genome mapping as a novel high-resolution typing tool for Legionella pneumophila.
Bosch T et al. J. Clin. Microbiol. 2015 Jul 22.

Genomically informed surveillance for carbapenem-resistant enterobacteriaceae in a health care system.
Pecora ND et al. MBio 2015 (4)

Early insights into the potential of the Oxford nanopore MinION for the detection of antimicrobial resistance genes.
Judge K et al. J. Antimicrob. Chemother. 2015 Jul 28.

Real-time PCR for detection of Strongyloides stercoralis in human stool samples from Côte d'Ivoire: diagnostic accuracy, inter-laboratory comparison and patterns of hookworm co-infection.
Becker SL et al. Acta Trop. 2015 Jul 24.

The use of next generation sequencing in the diagnosis and typing of respiratory infections.
Thorburn F et al. J. Clin. Virol. 2015 Aug 96-100

First international external quality assessment of molecular diagnostics for Mers-CoV.
Pas SD et al. J. Clin. Virol. 2015 Aug 81-5

Diagnostic microbiology: the accelerating transition from culture-based to molecular-based methods.
Wilson ML et al. Am. J. Clin. Pathol. 2015 Jun (6) 766-7

Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for identification and clustering of Neisseria gonorrhoeae.
Carannante A et al. BMC Microbiol. 2015 142

Molecular epidemiology of Mycoplasma pneumoniae: genotyping using single nucleotide polymorphisms and SNaPshot™ technology.
Touati A et al. J. Clin. Microbiol. 2015 Jul 22.

Evaluation of the biotyper MALDI-TOF MS system for identification of Staphylococcus species.
Zhu W et al. J. Microbiol. Methods 2015 Jul 13. 14-17

Top of Page

---

Epidemiology/ Outbreaks/ Transmission

Echovirus 30 meningitis epidemic followed by an outbreak-specific RT-qPCR.
Österback R et al. J. Clin. Virol. 2015 Aug 7-11

Investigation of a leptospirosis outbreak in triathlon participants, Réunion Island, 2013.
Pagès F et al. Epidemiol. Infect. 2015 Jul 27. 1-9

An outbreak of hepatitis A virus associated with a multi-national inner-city nursery in Glasgow, Scotland.
Li KK et al. J. Clin. Virol. 2015 Aug 12-5

HIV-1 diversity, transmission dynamics and primary drug resistance in Angola.
Bártolo I et al. PLoS ONE 2014 (12) e113626

Top of Page

---

Antimicrobials/ Vaccines/ Interventions

Campylobacter jejuni biofilms contain extracellular DNA and are sensitive to DNase I treatment.
Brown Helen L et al. Front Microbiol 2015 699

Imperfect Vaccination Can Enhance the Transmission of Highly Virulent Pathogens.
Read Andrew F et al. PLoS Biol. 2015 Jul (7) e1002198

Identification of hemagglutinin residues responsible for H3N2 antigenic drift during the 2014-2015 influenza season.
Chambers BS et al. Cell Rep 2015 Jul 7. (1) 1-6

Clinical features and viral kinetics in a rapidly cured patient with Ebola virus disease: a case report.
Schibler M et al. Lancet Infect Dis 2015 Jul 17.

Evaluation of candidate vaccine approaches for MERS-CoV.
Wang L et al. Nat Commun 2015 7712

Characterization of invasive Neisseria meningitidis strains from Québec, Canada, during a period of increased serogroup B disease, 2009-2013: phenotyping and genotyping with special emphasis on the non-carbohydrate protein vaccine targets.
Law DKS et al. BMC Microbiol. 2015 143

Top of Page

---

Host-Microbe Interactions

The Interplay Between Host Genetic Variation, Viral Replication, and Microbial Translocation in Untreated HIV-Infected Individuals.
Perkins Molly R et al. J. Infect. Dis. 2015 Aug 15. (4) 578-84

Exploring Host-Microbiome Interactions using an in Silico Model of Biomimetic Robots and Engineered Living Cells.
Heyde Keith C et al. Sci Rep 2015 11988

The airway microbiome in patients with severe asthma: Associations with disease features and severity.
Huang YJ et al. J. Allergy Clin. Immunol. 2015 Jul 25.

Hepatitis B virus genotype B and mutations in basal core promoter and pre-core/core genes associated with acute-on-chronic liver failure: a multicenter cross-sectional study in China.
Yang G et al. Hepatol Int 2014 Oct (4) 508-16

The female urinary microbiota in urgency urinary incontinence.
Pearce MM et al. Am. J. Obstet. Gynecol. 2015 Jul 22.