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

Genomics|Update|Infectious Diseases

Volume 35  Number 12  September 17-24, 2015

Advanced Molecular Detection in Action

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

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

News/ Reviews/ Commentaries

Sequencing of serial clinical pathogen isolates IDs SNV responsible for drug resistance
Heger M. GenomeWeb, Sep 11, 2015.

FDA clears Nanosphere's respiratory pathogen test
GenomeWeb, Sep 8, 2015.

Study results suggest overdiagnosis of C. difficile with molecular testing
Ashford M. GenomeWeb, Sep 15, 2015.

"Molecular tweeting" could hold the key to busting superbugs 
Greenemeier L. Sci Am, Aug 31, 2015.

NGS-based genome mining technique could identify new antibacterial compounds
Heger M. GenomeWeb, Sep 16, 2015.

Ten simple rules for a computational biologist's laboratory notebook.
Schnell S et al. PLoS Comput. Biol. 2015 Sep (9) e1004385

Molecular detection and point-of-care testing in Ebola virus disease and other threats: a new global public health framework to stop outbreaks.
Kost GJ et al. Expert Rev. Mol. Diagn. 2015 Sep 14. 1-15

Middle East Respiratory syndrome coronavirus recombination and the evolution of science and public health in China.
Lipkin WI et al. MBio 2015 (5)

Viral hemorrhagic fever diagnostics.
Racsa LD et al. Clin. Infect. Dis. 2015 Sep 9.

The great big clean-up
Grens K. The Scientist, Sep 1, 2015.

The road to hell is paved with bioinformatics formats 
Robison K. OMICS! OMICS!, Aug 26, 2015.

The cell menagerie: human immune profiling
Fessenden M. Nature, Sep 16, 2015.

Future directions for the European influenza reference laboratory network in influenza surveillance.
Goddard N et al. Euro Surveill. 2015 (30)

Ebola virus: Sensationalism, science, and human rights.
Bausch Daniel G et al. J. Infect. Dis. 2015 Oct 1. S79-83

Top of Page

---

Policy

Flu study raises questions about U.S. ban
Cohen J. Science, Sep 11, 2015.

Dual-use research of concern (DURC) review at American Society for Microbiology journals.
Casadevall A et al. MBio 2015 (4) e01236

Top of Page

---

Methods/Tools

Bayesian mixture analysis for metagenomic community profiling.
Morfopoulou S et al. Bioinformatics 2015 Sep 15. (18) 2930-8

High-throughput optical sensing of nucleic acids in a nanopore array.
Huang S et al. Nat Nanotechnol 2015 Aug 31.

Database of host-pathogen and related species interactions, and their global distribution
Wardeh M, et al. Sci Data 2015; 2:150049.

Concordance and discordance of sequence survey methods for molecular epidemiology.
Castro-N E et al. PeerJ 2015 e761

Single-molecule real-time sequencing combined with optical mapping yields completely finished fungal genome.
Faino L et al. MBio 2015 (4)

An improved reverse genetics system to overcome cell-type-dependent Ebola virus genome plasticity.
Tsuda Y et al. J. Infect. Dis. 2015 Oct 1. S129-37

Top of Page

---

Evolution/ Ecology/ Populations

Origin and possible genetic recombination of the Middle East Respiratory syndrome coronavirus from the first imported case in China: Phylogenetics and coalescence analysis.
Wang Yanqun et al. MBio 2015 (5)

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. 2015 Jul 26.

Complete genome sequences of three Neisseria gonorrhoeae laboratory reference strains, determined using PacBio single-molecule real-time technology.
Abrams AJ et al. Genome Announc 2015 (5) (CDC Author)

Norovirus genotype diversity associated with gastroenteritis outbreaks in aged-care facilities.
Bruggink LD et al. Epidemiol. Infect. 2015 Oct (14) 3064-8

Emergence of a new highly successful acapsular group A streptococcus clade of genotype emm89 in the United Kingdom.
Turner CE et al. MBio 2015 (4) e00622

A re-evaluation of the origin of hepatitis C virus genotype 2 in West Africa.
Purdy MA et al. J. Gen. Virol. 2015 Aug (8) 2157-64 (CDC Author)

Comparative genomic analyses of freshly isolated Giardia intestinalis assemblage A isolates.
Ankarklev J et al. BMC Genomics 2015 (1) 697

Phylogenetic analyzes of Influenza A (H1N1)pdm09 hemagglutinin gene during and after the pandemic event in Brazil.
Resende PC et al. Infect. Genet. Evol. 2015 Sep 11.

Evolutionary characterization of the emerging porcine epidemic diarrhea virus worldwide and 2014 epidemic in Taiwan.
Sung Ming-Hua et al. Infect. Genet. Evol. 2015 Sep 13.

Mitochondrial genome analyses suggest multiple trichuris species in humans, baboons, and pigs from different geographical regions.
Hawash MBF et al. PLoS Negl Trop Dis 2015 Sep (9) e0004059

Top of Page

---

Pathogenicity / Antimicrobial Resistance

Genome-wide transcription study of Cryptococcus neoformans H99 clinical strain versus environmental strains.
Movahed El et al. PLoS ONE 2015 (9) e0137457

Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia.
Pak TR et al. Antimicrob. Agents Chemother. 2015 Aug 31.

Rapid detection of B2-ST131 clonal group of extended-spectrum ?-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. 2015 Jul 29.

Strain features and distributions in pneumococci from children with invasive disease before and after 13 valent conjugate vaccine implementation in the United States.
Metcalf BJ et al. Clin. Microbiol. Infect. 2015 Sep 9. (CDC Author)

Molecular epidemiology of multidrug-resistant Acinetobacter baumannii isolates in a university hospital in Nepal reveals the emergence of a novel epidemic clonal lineage.
Shrestha S et al. Int. J. Antimicrob. Agents 2015 Aug 28.

Evolutionary trade-offs underlie the multi-faceted virulence of staphylococcus aureus.
Laabei M et al. PLoS Biol. 2015 Sep (9) e1002229

Comparative genomics between human and animal associated subspecies of the Mycobacterium avium complex: a basis for pathogenicity.
Timms VJ et al. BMC Genomics 2015 (1) 695

Differential gene expression and infection profiles of cutaneous and mucosal leishmania braziliensis isolates from the same patient.
Alves-Ferreira EVC et al. PLoS Negl Trop Dis 2015 Sep (9) e0004018

Top of Page

---

Detection/ Diagnosis

Overdiagnosis of clostridium difficile infection in the molecular test era.
Polage CR et al. JAMA Intern Med 2015 Sep 8. 1-10

Direct molecular testing to assess the incidence of meningococcal and other bacterial causes of meningitis among persons reported with unspecified bacterial meningitis.
Ramautar AE et al. Diagn. Microbiol. Infect. Dis. 2015 Jun 16.

Comparison between conventional culture and NAATs for the microbiological diagnosis in gonococcal infection.
Serra-Pladevall J et al. Diagn. Microbiol. Infect. Dis. 2015 Aug 8.

Multicolor melting curve analysis-based multilocus melt typing of vibrio parahaemolyticus.
Liu R et al. PLoS ONE 2015 (9) e0136998

Rapid first-line discrimination of methicillin resistant Staphylococcus aureus strains using MALDI-TOF MS.
Østergaard C et al. Int. J. Med. Microbiol. 2015 Aug 14.

Clinical performance of a matrix-assisted laser desorption ionization time-of-flight mass spectrometry method for the detection of certain blaKPC-containing plasmids.
Youn Jung-Ho et al. J. Clin. Microbiol. 2015 Sep 2.

Comparing MALDI-TOF MS, phenotypic and molecular methods for the identification of species within the Streptococcus anginosus group.
Arinto-Garcia R et al. J. Clin. Microbiol. 2015 Sep 9.

Fluorescence in situ hybridization for the identification of Treponema pallidum in tissue sections.
Petrich A et al. Int. J. Med. Microbiol. 2015 Aug 28.

Protocol for metagenomic virus detection in clinical specimens.
Kohl C et al. Emerging Infect. Dis. 2015 Jan (1) 48-57

Diagnostic accuracy of rapid antigen detection tests for respiratory syncytial virus infection: systematic review and meta-analysis.
Chartrand C et al. J. Clin. Microbiol. 2015 Sep 9.

Development of prototype filovirus recombinant antigen immunoassays.
Boisen ML et al. J. Infect. Dis. 2015 Oct 1. S359-67

Analysis of breath specimens for biomarkers of plasmodium falciparum infection.
Berna AZ et al. J. Infect. Dis. 2015 Oct 1. (7) 1120-8

Top of Page

---

Epidemiology/ Outbreaks/ Transmission

The role of sequencing of the heamagglutinin gene and the hypervariable region in the measles outbreak investigations in Sweden, 2013-2014.
Harvala H et al. J. Infect. Dis. 2015 Sep 7.

Case-based surveillance enhanced with measles virus detection/genotyping is essential to maintain measles elimination in Aichi Prefecture, Japan.
Minagawa H et al. Vaccine 2015 Sep 3. 

Use of sequence analysis of the P2 domain for characterization of norovirus strains causing a large multistate outbreak of norovirus gastroenteritis in Germany 2012.
Höhne M et al. Int. J. Med. Microbiol. 2015 Aug 21.

Molecular epidemiology of Brucella abortus in Northern Ireland-1991 to 2012.
Allen A et al. PLoS ONE 2015 (9) e0136721

Phylogeographical pattern of Francisella tularensis in a nationwide outbreak of tularaemia in Norway, 2011.
Afset JE et al. Euro Surveill. 2015 (19) 9-14

European surveillance for enterovirus D68 during the emerging North-American outbreak in 2014.
Poelman R et al. J. Clin. Virol. 2015 Oct 1-9

The utility of whole genome sequencing of Escherichia coli O157 for outbreak detection and epidemiological surveillance.
Holmes A et al. J. Clin. Microbiol. 2015 Sep 9.

Whole-genome sequencing for tracing the transmission link between two ARD outbreaks caused by a novel HAdV serotype 7 variant, China.
Qiu S et al. Sci Rep 2015 13617

Top of Page

---

Antimicrobials/ Vaccines/ Interventions

Emergence of Ebola virus escape variants in infected nonhuman primates treated with the MB-003 antibody cocktail.
Kugelman JR et al. Cell Rep 2015 Sep 9.

Longitudinal detection and persistence of minority drug-resistant populations and their effect on salvage therapy.
Nishizawa M et al. PLoS ONE 2015 (9) e0135941 (CDC Author)

Glycosylation analysis of engineered H3N2 influenza A virus hemagglutinins with sequentially added historically relevant glycosylation sites.
An Y et al. J. Proteome Res. 2015 Sep 4. (9) 3957-69 (CDC Author)

Top of Page

---

Host-Microbe Interactions

Human genetic ancestral composition correlates with the origin of Mycobacterium leprae strains in a leprosy endemic population.
Cardona-Castro N et al. PLoS Negl Trop Dis 2015 Sep (9) e0004045

Gut DNA viromes of Malawian twins discordant for severe acute malnutrition.
Reyes A et al. Proc. Natl. Acad. Sci. U.S.A. 2015 Sep 8.

MICROBIOME. Rethinking heritability of the microbiome.
van Opstal EJ et al. Science 2015 Sep 11. (6253) 1172-3

The human skin microbiome associates with the outcome of and is influenced by bacterial infection
van Rensburg JJ, et al. mBio, Sep 15, 2015.

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples.
Korem T et al. Science 2015 Sep 4. (6252) 1101-6

Excessive cytolytic responses predict tuberculosis relapse after apparently successful treatment.
Cliff JM et al. J. Infect. Dis. 2015 Sep 7.

IFITM3 rs12252 T>C polymorphism is associated with the risk of severe influenza: a meta-analysis.
Xuan Y et al. Epidemiol. Infect. 2015 Oct (14) 2975-84

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls.
Castro-Nallar E et al. PeerJ 2015 e1140

The initial state of the human gut microbiome determines its reshaping by antibiotics.
Raymond F et al. ISME J 2015 Sep 11.

Influence of genetic ancestry on INDEL markers of NFKβ1, CASP8, PAR1, IL4 and CYP19A1 genes in leprosy patients.
Pinto P et al. PLoS Negl Trop Dis 2015 Sep (9) e0004050

Frenemies: Signaling and nutritional integration in pathogen-microbiota-host interactions.
Cameron EA et al. Cell Host Microbe 2015 Sep 9. (3) 275-84

Pathogenic role of human herpesvirus 6B infection in mesial temporal lobe epilepsy.
Kawamura Y et al. J. Infect. Dis. 2015 Oct 1. (7) 1014-21