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

Genomics|Update|Infectious Diseases

Volume 35  Number 3  July 16-23, 2015

Advanced Molecular Detection in Action

• Antimicrobials/ Vaccines/ Interventions
• Detection/ Diagnosis
• Epidemiology/ Outbreaks/ Transmission
• Evolution/ Ecology/ Populations

• Host-Microbe Interactions
• Methods/ Tools
• Pathogenicity / Antimicrobial Resistance
• Policy
• Reviews/ News/ Commentaries

Antimicrobials/ Vaccines/ Interventions

A perspective on genomic-guided anthelmintic discovery and repurposing using Haemonchus contortus.
Preston S et al. Infect. Genet. Evol. 2015 Jul 3.

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Detection/ Diagnosis

Economic analysis of rapid and sensitive polymerase chain reaction testing in the emergency department for influenza infections in children
Nelson RE, et al. Pediatric Infectious Disease Journal 2015 June

Comparison of FilmArray® and qRT-PCR for the detection of Zaire ebolavirus from contrived and clinical specimens.
Southern TR et al. J. Clin. Microbiol. 2015 Jul 8. (CDC Author)

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry identification of large colony beta-hemolytic streptococci containing Lancefield groups A, C, and G.
Jensen CS et al. Infect Dis (Lond) 2015 Aug (8) 575-9

Comparative genome analysis identifies novel nucleic acid diagnostic targets for use in the specific detection of Haemophilus influenzae.
Coughlan H et al. Diagn. Microbiol. Infect. Dis. 2015 Jun 23.

An 11,000-isolate same plate/same day comparison of the 3 most widely used platforms for analyzing multidrug-resistant clinical pathogens.
Nielsen LE et al. Diagn. Microbiol. Infect. Dis. 2015 Jun 11.

Development of a pan-serotype reverse transcription loop-mediated isothermal amplification assay for the detection of dengue virus.
Dauner AL et al. Diagn. Microbiol. Infect. Dis. 2015 May 15.

Detection of Vibrio cholerae O1 and O139 in environmental waters of rural Bangladesh: a flow-cytometry-based field trial.
Righetto L et al. Epidemiol. Infect. 2015 Aug (11) 2330-42

Polymerase chain reaction-based active surveillance of MRSA in emergency department patients.
Seki M et al. Infect Drug Resist 2015 113-8

Cryptic hepatitis B and E in patients with acute hepatitis of unknown etiology.
Ganova-Raeva L et al. J. Infect. Dis. 2015 Jun 8. (CDC Author)

Molecular characterization of Leptospira sp. by multi locus VNTR analysis (MLVA) from clinical samples: a case report.
Pailhoriès H et al. Int. J. Infect. Dis. 2015 Jul 6.

Rapid and sensitive isothermal detection of nucleic-acid sequence by multiple cross displacement amplification.
Wang Yi et al. Sci Rep 2015 11902

Detection and quantification of airborne norovirus during outbreaks in healthcare facilities.
Bonifait L et al. Clin. Infect. Dis. 2015 Apr 21.

Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains
Lewandowska DW, et al. Diagn Microbiol Infect Dis, Jun 29, 2015. 

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Epidemiology/ Outbreaks/ Transmission

A variegated squirrel bornavirus associated with fatal human encephalitis 
Hoffmann B, et al. New Engl J Med 2015; 373:154-162 July 9, 2015

Targeting prevention based on molecular epidemiology among deeply sampled sub-networks of men have who sex with men.
Wang X et al. Clin. Infect. Dis. 2015 Jun 30.

Phylogenetic analysis of highly pathogenic avian influenza A(H5N8) virus outbreak strains provides evidence for four separate introductions and one between-poultry farm transmission in the Netherlands, November 2014.
Bouwstra RJ et al. Euro Surveill. 2015 (26)

Bottlenecks in HIV-1 transmission: insights from the study of founder viruses.
Joseph SB et al. Nat. Rev. Microbiol. 2015 Jul (7) 414-25

Tracking a hospital outbreak of KPC-producing ST11 Klebsiella pneumoniae with whole-genome sequencing.
Jiang Y et al. Clin. Microbiol. Infect. 2015 Jul 9.

Molecular epidemiology of a post-influenza pandemic outbreak of acute respiratory infections in Korea caused by human adenovirus type 3.
Lee Wan-Ji et al. J. Med. Virol. 2015 Jan (1) 10-7

Whole genome sequencing provides an unambiguous link between Salmonella Dublin outbreak strain and a historical isolate.
Mohammed M et al. Epidemiol. Infect. 2015 Jul 13. 1-6

Whole-genome sequencing of measles virus genotypes H1 and D8 during outbreaks of infection following the 2010 Olympic Winter Games reveals viral transmission routes.
Gardy JL et al. J. Infect. Dis. 2015 Jul 6.

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Evolution/ Ecology/ Populations

Influenza A viruses of human origin in swine, Brazil 
Nelson MI, et al. Emerg Infect Dis, Aug 2015.

Putative lineage of novel African Usutu virus, Central Europe 
Cadar D, et al. Emerg Infect Dis, Sep 2015.

Emergence of a new highly successful acapsular group A streptococcus clade of genotype emm89 in the United Kingdom 
Turner CE, et al. mBio 2015; 6(4): e00622-15.

Phylogenetic study of clonal complex (CC)198 capsule null locus (cnl) genomes: a distinctive group within the species Neisseria meningitidis.
Xu Z et al. Infect. Genet. Evol. 2015 Jul 11.

Phylogenetic study reveals co-circulation of Asian II and Cosmopolitan genotypes of Dengue virus serotype 2 in Nepal during 2013.
Singh S et al. Infect. Genet. Evol. 2015 Jul 6.

Using whole genome analysis to examine recombination across diverse sequence types of Staphylococcus aureus.
Driebe EM et al. PLoS ONE 2015 (7) e0130955

Comparison of genomic signatures of selection on Plasmodium falciparum between different regions of a country with high malaria endemicity.
Duffy CW et al. BMC Genomics 2015 527

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Host-Microbe Interactions

Impairment of immunity to Candida and Mycobacterium in humans with bi-allelic RORC mutations 
Okada S, et al. Science, July 9, 2015.

High-level of viral genomic diversity in cervical cancers: a Brazilian study on Human Papillomavirus type 16
de Oliveira CM, et al. Infect Genet Evol, Jul 6, 2015.

Antibiotic-induced alterations of the murine gut microbiota and subsequent effects on colonization resistance against Clostridium difficile
Schubert AM, et al. mBio 2015; 6(4): e00974-15.

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment.
Burns MB et al. Genome Med 2015 (1) 55

High-level of viral genomic diversity in cervical cancers: A Brazilian study on human papillomavirus type 16.
de Oliveira CM et al. Infect. Genet. Evol. 2015 Jul 6.

The lung microbiome: New principles for respiratory cacteriology in health and disease.
Dickson RP et al. PLoS Pathog. 2015 Jul (7) e1004923

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Methods/Tools

Good laboratory practice for clinical next-generation sequencing informatics pipelines
Gargis A, et al. Nature Biotechnology 2015; 33, 689?693. (CDC Author)

A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status.
Greiff V et al. Genome Med 2015 (1) 49

Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data.
Sahl JW et al. Genome Med 2015 (1) 52

Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples.
Matranga CB et al. Genome Biol. 2014 (11) 519

Development of a reverse genetics system to generate a recombinant Ebola virus Makona expressing a green fluorescent protein.
Albariño CG et al. Virology 2015 Jun 26. 259-264 (CDC Author)

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Pathogenicity / Antimicrobial Resistance

Genotypes and antibiotic resistance of bovine Campylobacter and their contribution to human campylobacteriosis.
Jonas R et al. Epidemiol. Infect. 2015 Aug (11) 2373-80

Between a bug and a hard place: Trypanosoma cruzi genetic diversity and the clinical outcomes of Chagas disease.
Messenger LA et al. Expert Rev Anti Infect Ther 2015 Aug (8) 995-1029

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

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

Model-based clustering of Escherichia coli O157:H7 genotypes and their potential association with clinical outcome in human infections
Elhadidy M, et al. Diagn Microbiol Infect Dis, Jun 29, 2015.

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Policy

International infectious disease emergencies and domestic implications for the public health and health care sectors: Workshop in brief 
(report) Institute of Medicine, Jul 2015.

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Reviews/ News/ Commentaries

Researchers develop genetic tools to engineer common gut bacterium
GenomeWeb, Jul 9, 2015.

Fluidigm, OpGen ink deal to develop multi-drug resistance test equipment and kits
GenomeWeb, Jul 13, 2015.

GWU team aims to build gut microbiome analysis service
Macron D. GenomeWeb, Jul 10, 2015.

Team IDs new virus with apparent ties to deadly encephalitis cases in imported squirrel reservoir
Anderson A. GenomeWeb, Jul 9, 2015.

NY DOH develops multiplex real-time PCR to combat staph food poisoning, bioterrorism
Johnson M. GenomeWeb, Jul 15, 2015.

Thermo Fisher Partners with CDC to develop software for MicrobeNet database
GenomeWeb, Jul 16, 2015.

Researchers develop world's most sensitive test to detect infectious disease, superbugs
Phys.org, Jul 6, 2015.

Could bacteria be turned into living medical devices?
Sturgis K. Qmed, Jul 13, 2015.

Genome watch: The chronicles of virus-host affairs.
Langat P et al. Nat. Rev. Microbiol. 2015 Jul 13.

Viral evolution: Keeping a watchful eye on Ebola.
Attar N et al. Nat. Rev. Microbiol. 2015 Jul 6.

Whole-Genome Sequencing During Measles Outbreaks.
Rota PA et al. J. Infect. Dis. 2015 Jul 6. (CDC Author)

Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases?
Van Borm S et al. Methods Mol. Biol. 2015 415-36

Parasitology: CRISPR for Cryptosporidium
Beverley SM. Nature, Jul 15, 2015.